Kdraeder/fix st archive #1916

kdraeder · 2017-09-22T22:46:50Z

_get_ninst_info; comment out else: ninst_strings.append('')
Appends 2 single quotes, instead of nothing as intended.
_get_component_archive_entries: add log info about components that are skipped.
_archive_rpointer_files: debugging statements in can eventually be removed.
_archive_history_files, _archive_restart_date_comps:
changed handling of 'dart' compname to 'esp'
and use fact that DART output, which st_archive should archive,
now all uses standard CESM naming conventions.
Updated logger information.

Test suite: scripts_regression_tests
Test baseline: cime5.3.0-alpha.33
Test namelist changes: none
Test status: bit for bit

Fixes #1854

User interface changes?: none

Update gh-pages html (Y/N)?:

Code review: it needs one

jedwards4b · 2017-09-22T23:04:57Z

In the initial comment you need to remove the code in [] and replace it. So

[ Description of the changes ...

should be replaced with a human readable summary of the changes and

Fixes [CIME Github issue #]

should be replaced with

Fixes #1854

the format of the Fixes line is important for some automated github interaction.

Just for testing.

> _get_ninst_info; comment out else: ninst_strings.append('') Appends 2 single quotes, instead of nothing as intended. > _get_component_archive_entries: add log info about components that are skipped. > _archive_rpointer_files: debugging statements in can eventually be removed. > _archive_history_files, _archive_restart_date_comps: changed handling of 'dart' compname to 'esp' and use fact that DART output, which st_archive should archive, now all uses standard CESM naming conventions. Updated logger information.

jedwards4b · 2017-09-22T23:11:01Z

scripts/lib/CIME/case_st_archive.py

@@ -67,8 +67,10 @@ def _get_ninst_info(case, compclass):
    for i in range(1,ninst+1):
        if ninst > 1:
            ninst_strings.append('_' + '{:04d}'.format(i))
-        else:
-            ninst_strings.append('')
+# KDR This doesn't do what's intended.  The result is ninst_strings is not empty.


remove commented code

This commented code still needs to be removed.

jedwards4b · 2017-09-22T23:11:22Z

scripts/lib/CIME/case_st_archive.py

@@ -90,6 +92,10 @@ def _get_component_archive_entries(case, archive):
        if archive_entry is not None:
            yield(archive_entry, compname, archive_entry.get("compclass"))

+    if compname not in compset_comps:
+        # KDR Say if something is being skipped


No need for comment

I don't understand the intent of this. Will this ever get triggered? I'm confused because, i the above loop, compname takes on the various values of compset_comps. I can't understand any scenario where compname down here would not be something in compset_comps. Maybe this was a debugging statement that you meant to remove?

jedwards4b · 2017-09-22T23:11:44Z

scripts/lib/CIME/case_st_archive.py

@@ -121,27 +127,36 @@ def _archive_rpointer_files(case, archive, archive_entry, archive_restdir,
                temp_rpointer_content = rpointer_content
                # put in a temporary setting for ninst_strings if they are empty
                # in order to have just one loop over ninst_strings below
-                if rpointer_content is not 'unset':
+                # KDR 'is not' queries whether they are the same object.


Comment refers to code that is not here, please remove

jedwards4b · 2017-09-22T23:13:41Z

scripts/lib/CIME/case_st_archive.py

-                    for output in rpointer_content.split(','):
-                        f.write("{} \n".format(output))
-                    f.close()
+                    # KDR indented 4 spaces, up to 'else:' to put under control of 'if ... unset'


Don't put KDR in comments, this comment should be removed.

jedwards4b · 2017-09-22T23:14:30Z

scripts/lib/CIME/case_st_archive.py

+                            f.write("{} \n".format(output))
+                        f.close()
+                else:
+                    # KDR debugging why rpointer.unset are being created.


Should this logger.info be removed then? ie is it only for debug?

jedwards4b · 2017-09-22T23:15:11Z

scripts/lib/CIME/case_st_archive.py

@@ -327,6 +345,11 @@ def _archive_restarts_date_comp(case, archive, archive_entry,
                pattern = compname + suffix + '_'.join(datename.rsplit('-', 1))
                pfile = re.compile(pattern)
                restfiles = [f for f in os.listdir(rundir) if pfile.search(f)]
+# KDR CAM+DART doesn't need special treatment as of 2017-9-1, so this is commented out.


just remove this

jedwards4b · 2017-09-22T23:15:35Z

scripts/lib/CIME/case_st_archive.py

-                newsuffix = compname + '.*' + suffix
+            if compname.find('mpas') == 0:
+               newsuffix = compname + '.*' + suffix
+# KDR I've chosen to use compname 'cam' for DART output from CAM assims,


Remove comment

jedwards4b · 2017-09-22T23:16:03Z

scripts/lib/CIME/case_st_archive.py

                else:
                    # Only archive intermediate restarts if requested - otherwise remove them
                    if case.get_value('DOUT_S_SAVE_INTERIM_RESTART_FILES'):
                        srcfile = os.path.join(rundir, restfile)
                        destfile = os.path.join(archive_restdir, restfile)
-                        logger.info("moving \n{} to \n{}".format(srcfile, destfile))
+# KDR redundant?                        logger.info("moving \n{} to \n{}".format(srcfile, destfile))


Remove comment, not needed.

jedwards4b

Comments in the code with initials (KDR) or refering to code that is no longer present in the source tend to confuse rather than clarify. If you wanted to indicate to reviewers why you made the changes that you did. This PR review process works for that. Also I did a force update of your branch to incorporate the latest master code which already had your fix to case_setup.py applied.

kdraeder · 2017-09-23T01:46:23Z

Thanks for the guidance. Any more suggestions?
Since the Github version of fix_st_archive has been updated,
I need to pull that to my local version. Where do I find the
right Github repository name, path, address, ...?

billsacks · 2017-09-23T12:49:03Z

@kdraeder to add a bit to what @jedwards4b said: After submitting a PR, you can insert line comments explaining what you did.

@jedwards4b I think we should really try to avoid doing force updates to other people's branches (if I'm understanding you right that you did something like git push ... --force): this can make life difficult for others.

billsacks · 2017-09-23T12:53:53Z

scripts/lib/CIME/case_st_archive.py

@@ -90,6 +92,10 @@ def _get_component_archive_entries(case, archive):
        if archive_entry is not None:
            yield(archive_entry, compname, archive_entry.get("compclass"))

+    if compname not in compset_comps:
+        # KDR Say if something is being skipped


I don't understand the intent of this. Will this ever get triggered? I'm confused because, i the above loop, compname takes on the various values of compset_comps. I can't understand any scenario where compname down here would not be something in compset_comps. Maybe this was a debugging statement that you meant to remove?

billsacks · 2017-09-23T12:58:19Z

scripts/lib/CIME/case_st_archive.py

+                # if rpointer_content is not 'unset':
+                if rpointer_content != 'unset':
+                    # KDR debugging why rpointer.unset are being created.
+                    logger.info("rpointer_content not unset? {}".format(rpointer_content))


Did you mean for this to stay in the final version? If so, should it be done with something like logger.debug rather than logger.info?

billsacks · 2017-09-23T13:04:23Z

scripts/lib/CIME/case_st_archive.py

+#     inside compclass 'esp', to distinguish it from other components in multi-component assims.
+#     All CAM+DART output conforms to CESM naming conventions (2017-9-1).
+            elif ninst_string:
+               newsuffix = casename + '.' + compname + ".*" + ninst_string[i] + suffix


I think you meant to remove the following, which is now redundant:

if ninst_string: newsuffix = casename + '.' + compname + ".*" + ninst_string[i] + suffix else:

billsacks · 2017-09-23T13:05:19Z

scripts/lib/CIME/case_st_archive.py

-            elif compname.find('mpas') == 0:
-                newsuffix = compname + '.*' + suffix
+            if compname.find('mpas') == 0:
+               newsuffix = compname + '.*' + suffix


While this is not a new problem, I'm wondering if this logic is correct with respect to mpas: It looks to me like this code block cannot handle having an mpas component together with multi-instance?

kdraeder · 2017-09-25T17:51:18Z

I'm still trying to figure out the form of the repository version, from which
I want to pull the changes that @jedwards4b applied to the Github branch.
I've found some syntax in the git-pull help page:
http[s]://host.xz[:port]/path/to/repo.git/
but I don't know what to fill in for what parts of that, or if that's even the right form.
Thanks for any guidance.
Kevin

jedwards4b · 2017-09-25T19:07:19Z

@kdraeder I think that if you bring your laptop down to my office we can go over it togther
@billsacks I don't know of a way to rebase without doing a force push - do you?

billsacks · 2017-09-25T19:20:35Z

@jedwards4b right; the more general rule is that we shouldn't rebase or otherwise rewrite history of someone else's branch.

See https://git-scm.com/book/en/v2/Git-Branching-Rebasing

The Perils of Rebasing

Ahh, but the bliss of rebasing isn’t without its drawbacks, which can be summed up in a single line:

Do not rebase commits that exist outside your repository.

If you follow that guideline, you’ll be fine. If you don’t, people will hate you, and you’ll be scorned by friends and family.

When you rebase stuff, you’re abandoning existing commits and creating new ones that are similar but different. If you push commits somewhere and others pull them down and base work on them, and then you rewrite those commits with git rebase and push them up again, your collaborators will have to re-merge their work and things will get messy when you try to pull their work back into yours.

rljacob · 2017-09-25T19:24:49Z

The key is "if others pull them down and base work off them". If you know no one did that or you can contact them its ok to rebase a public branch. For widely used software like the Linux kernel, you definitely can't rebase a public branch. For CIME, its probably ok.

billsacks · 2017-09-25T19:28:29Z

@rljacob I agree. I have no problems with people rebasing their own branches if they are pretty sure that nobody else has been working on those branches. I am not okay with other people rebasing my branches unless I give permission. In those situations, they should either use a merge or create a completely new branch.

rljacob · 2017-09-25T19:42:02Z

Agreed.

bertinia

I think @billsacks and @jedwards4b have commented on all the changes that need to be addressed.

kdraeder · 2017-09-26T20:06:09Z

Ready for new review.
Jim helped me merge the updated Github version
with my local version, which has fixed based on reviews.

jedwards4b

All of the comments that I thought should be removed are still in case_st_archive.py

jedwards4b · 2017-09-26T20:09:02Z

scripts/lib/CIME/case_st_archive.py

@@ -67,8 +67,10 @@ def _get_ninst_info(case, compclass):
    for i in range(1,ninst+1):
        if ninst > 1:
            ninst_strings.append('_' + '{:04d}'.format(i))
-        else:
-            ninst_strings.append('')
+# KDR This doesn't do what's intended.  The result is ninst_strings is not empty.


This commented code still needs to be removed.

kdraeder · 2017-09-26T22:09:08Z

The merge we did must have overwritten my local changes.
We did a 'git pull origin', which failed because of my local changes.
Then we did 'git stash' and 'git reset origin/kdraeder/fix_st_archive'
without --hard. Did that overwrite my changes?
Is there any way to retrieve my changes in git, or do I have to recreate them?
Kevin

jedwards4b · 2017-09-26T22:21:14Z

I'm sorry - I think that we lost them, my fault.

jedwards4b · 2017-09-27T00:41:44Z

@billsacks point is well taken, I should have coordinated with @kdraeder before doing a force push.

kdraeder · 2017-09-27T19:19:24Z

I've re-installed the changes and run scripts_regression_test.py again.
There's a lot of output, and I don't know where to look to see how
successful it was, except that the last printed output says

Ran 113 tests in 3480.193s
FAILED (failures=2, skipped=8)
pylint version 1.5 or newer not found, pylint tests skipped
...
Detected failures, leaving directory:
/glade/scratch/raeder/scripts_regression_test.20170927_115119

I have not pushed the changes to kdraeder/fix_st_archive yet,
pending the evaluation of the test.

billsacks · 2017-09-27T19:24:01Z

@kdraeder I see failures in your output by grepping for FAIL:

FAIL: test_bless_test_results (__main__.Q_TestBlessTestResults)

FAIL: test_rebless_namelist (__main__.Q_TestBlessTestResults)

Why these two failed is another question... were these passing for you before?

billsacks · 2017-09-27T19:26:06Z

Actually, my guess is that scripts_regression_tests is trying to write to the real baseline area, and you don't have permissions there... I'm about to open an issue for that.

billsacks · 2017-09-27T19:30:02Z

Okay, #1928 opened. @kdraeder I'd say go ahead and push your changes. I could try rerunning Q_TestBlessTestResults to make sure it passes for me.

…ailures in scripts_regression_tests.py, but probably not related to case_st_archive.py changes.

billsacks

One remaining request, otherwise looks good - thank you!

I'm running the Q tests myself now, and will post when those have completed.

billsacks · 2017-09-27T21:41:25Z

scripts/lib/CIME/case_st_archive.py

@@ -90,6 +88,9 @@ def _get_component_archive_entries(case, archive):
        if archive_entry is not None:
            yield(archive_entry, compname, archive_entry.get("compclass"))

+    if compname not in compset_comps:
+        logger.debug('Skipping compname %s; it is not in compset_comps' %(compname))


My earlier comment still stands here:

I don't understand the intent of this. Will this ever get triggered? I'm confused because, in the above loop, compname takes on the various values of compset_comps. I can't understand any scenario where compname down here would not be something in compset_comps. Maybe this was a debugging statement that you meant to remove?

Can you either remove these two lines or explain the intent?

I did put it in as a debugging statement because there were problems
implementing short-term archiving of component esp before it was 'esp'.
There are other debugging statements in this module like this one,
so I thought it would be useful to leave it in. If it doesn't fit with the philosophy
of the scripts, I'm happy to take it out.
Kevin

I don't mind debugging statements in general - I'm just having a hard time seeing how this one could possibly get triggered: compname just loops through compset_comps, so under what circumstances could it ever be the case that compname is not in compset_comps?

Doh! I moved this from another, superseded routine, where compname was defined
independently of the for loop. I don't know where it would fit now, so I'll delete it.
Thanks for being persistent.

billsacks · 2017-09-27T21:49:12Z

scripts/lib/CIME/case_st_archive.py

-                newsuffix = compname + '.*' + suffix
+            if ninst_string:
+               if compname.find('mpas') == 0:
+                  # Not correct, but MPAS' multi-instance name format is unknown.


fyi I have opened #1931 for this

billsacks · 2017-09-27T22:27:55Z

Okay, the Q tests pass for me:

test_bless_test_results (__main__.Q_TestBlessTestResults) ... ok
test_rebless_namelist (__main__.Q_TestBlessTestResults) ... ok

billsacks · 2017-09-28T18:25:06Z

Okay, looks good to me now - thank you!

@bertinia did you want to review this before I merge it?

kdraeder · 2017-09-28T22:07:06Z

I believe that #1854, #1375 and #1374 may be resolved by this code.

f52ade075 Merge pull request #1974 from jedwards4b/fix_scalar_write_issue 3661a58bd derecho test script update 155be2fc9 update version 8b04e206f fix test for netcdf4 40bb45168 more github 1026fbd97 github tests again f01d36812 github tests again ab6c84b29 github tests again f1abc92cd github tests again d616e352a github tests again 3e6a435ad github tests again 20f1bcf94 github tests again 803298715 github tests again 24a9e1338 work on github tests e8d1be883 add derecho_testsuite.py 0ddbc2b8c fix scalar write issue, fix serial build issue 6d52a8c7d Merge pull request #1973 from jedwards4b/update/2.6.1 d9b6920e4 Merge branch 'main' into update/2.6.1 96a7d73d1 Merge pull request #1968 from jedwards4b/add_rpath 3d3a2f5dd Merge branch 'add_rpath' of github.com:jedwards4b/ParallelIO into add_rpath 3a4bfe06a resolve merge conflict ec1aef2c1 Merge branch 'main' into add_rpath 93b464bce update version 05e428451 Merge pull request #1972 from jedwards4b/bugfix/lustre 71b1fd248 try workflow again f377cab5c more workflow 10d4c3c67 fix for intel workflow 5b4717826 fix for intel workflow a42946660 add this back with a twist aa504dc8d add tmate for debugging workflows 513dbc8d0 fix ifort 1b68ba751 more cleanup 0bafcb4aa remove unused variables b4cb1ac34 update versions for github testing 3cf6ef570 clean up warnings 103a90991 more fixes for netcdf serial c45c4406a some fixes for netcdf serial bld 2cbf4bd0d potential fix for issue in branch bugtest/lustre 25b471d58 code changes to demo lustre performance bug ff7a19f21 add rpath variables to cmake build f45ba898b Merge pull request #1963 from jedwards4b/pio2.6.0rc1 a644bb61e update version d858d79d5 Merge pull request #1953 from jedwards4b/netcdf_integration_v5 4ac2b0e07 confusion about spack version 4fe8d187e confusion about spack version 020bfa712 skip test timeout pio_rearr_opts 2bd2c5d00 @develop should be @=develop (new change in spack)" ac3b0595b fix spack? 5e7a91e26 fix action b5244a576 spelling error 52e31e60a smarter about building parallelio 4003a79ea try this e0befe62b add tmate to debug eaffcf10f fix have_par_filters e437a94e7 fix some tests 95d9cf5c4 try this bc9534cb3 still trying bb08a8ff9 Merge branch 'main' into netcdf_integration_v5 cd8d7dbe9 remove unused arg 11c179e38 change test for par filters 11fc9d0a3 fix ifdef in fortran 38b8fef66 remove unused variable f240e34ef wrap filter_info 53462645c more cleanup 7390ec03d update autotools 77b579907 more cleanup f49d8ffbc reduce compiler warnings 3732b7c2b add test 3a0b1cd94 commit to move to gust 744bf5c3e Merge pull request #1962 from NCAR/jedwards4b-patch-1 c11ae47e9 Update README.md 44ab3d79b add pre-commit hook 30c3018a7 reorder to fix syntax error cdb55c733 prepare for pio 2.6.0 a5cbb28a6 add these and go to hackathon branch ad613dc55 add szip a16ca795f WIP 6af9cc985 cmake builds again 86101f2de add test for nc_inq_filter_avail 7119ddac7 more macro fixes 2247b3e65 more macro fixes fc8015f95 fix macros aede8723c fix testing again c0b49af55 add filter and quantize to fortran interface 02268a9fc add filter and quantize functionality 21cb6675d fix intel netcdf-c build f48a38b93 add back netcdf build 8c95ae17a try this 19e071bbe work on testing workflow 40ae6f019 update actions 152a0cf62 update actions cfc271e7c update actions 3b47163a6 update actions 6f88afa3b make it backward compatible 18eca188e fix the test 83176df55 add test, expected to fail 11a68cbd5 more fixes 6cf3810fe more fixes bd4517351 skip this test 6bb3a9b02 skip the check 93d82ad5e try again 3ffdd8124 more debugging 68b9a646b more debugging ab4ee59f5 try this 977ef90bf more fortran fixes dae38cdef more fortran fixes 3030489ea more fortran fixes cf92770d1 more fortran fixes dbc46c3f2 more fortran fixes ff513fbef fix fortran warnings 99fb47ac2 make it backward compatible abe19445a fix fortran warnings 6c8aad764 fix fortran warnings 54c3b8fab fix fortran warnings d0b8e5ebe fix fortran warnings 03079e75f fix fortran warnings 060fee736 make it backward compatible 09c5ded0a resolve merge conflicts d69dbe0ac passing all tests with NC_DISPATCH_VERSION=5 753464d2e fix declarations 77055f9e1 commit to try on cheyenne 7bce0e534 only run ncint tests for netcdf4 in netcdf4.9.0 and older 1747a4758 adding new filter functions 52649df69 determined test failure due to mpt/2.25 bug 781978d99 support versions 2-5 620f6741b Merge branch 'netcdf_integration_v5' of github.com:jedwards4b/ParallelIO into netcdf_integration_v5 3fd1b3e4e fix parens c404de8dd Merge branch 'main' into netcdf_integration_v5 2275ad951 stuck in testing 05173a655 Merge pull request #1952 from jedwards4b/master_to_main d3f134936 replace master with main 2446bf96c Merge pull request #1951 from jedwards4b/external_actions_squash 4fc7cd3d4 with -> enable e3e3ca7b8 fix type in workflow 4bdd79ca8 fix cache 1288017de squash commit of external_actions fd1bdf842 Merge pull request #1949 from jedwards4b/pio2.5.10-candidate 21a0f7015 update version patch to 10 126beaeee Merge pull request #1944 from billsacks/fix_default_mode 64666d199 Merge branch 'master' into fix_default_mode 6fcb613a2 Merge pull request #1946 from jedwards4b/update_github_tests c73a4d63c remove redundant test 490565b4f once more 2f95d78aa fix ldflags d1138cb57 try ldflags 79df169fe try fflags instead 20a223277 add -static-libasan 830f226bf remove memory violating comment b7745d637 update address sanitizer runs 74203a41b oops wrong hdf5 version 53c6eec31 more github action tuning acc462641 more github mods 87e0e9432 netcdf integration currently only works with netcdf-c 4.7.4 6f5d6b340 need both FFLAGS and FCFLAGS? 647e68cdd try this 9a9db159b try this 877f691c7 try this 5a4d06c11 more github action fixes 0eac1ebb9 try run-name here 8abc70dc7 fix yaml formatting issues a2a7a1132 change FCFLAGS to FFLAGS ce5faf9cb try removing name and adding run_name 0e91b5e4d remove name use run_name dee848ba1 update checkout and cache actions 9a63af64f update run-name 2fafb1581 update software versions 95553d71f update github tests to use -fallow-argument-mismatch bbfe1b221 Fix default value of mode for PIO_openfile df1c069fa Merge pull request #1941 from ACCESS-NRI/pkg-config 48baa2b29 backup search of NetCDF using PkgConfig 157e559ff Merge pull request #1937 from jedwards4b/cmake_version_revert eef316fb2 make work with cmake 3.5.2 (esmf requirement) a61c76304 Merge pull request #1936 from jedwards4b/version_update a342a931d update version tags 6ab657ab5 Merge pull request #1935 from jedwards4b/update/spack_experiences df5ced6e8 shared lib as default leads to problems linking gptl 586fd2509 add CMAKE_POSITION_INDEPENDENT_CODE 9fd941936 Merge branch 'master' into update/spack_experiences f43b5a8d8 Merge pull request #1928 from kgerheiser/patch-1 e96aa094a change malloc to calloc for tmparray 66478b875 updates based on experiences with spack package f18736b64 Merge branch 'master' into patch-1 07d5d1658 Merge pull request #1932 from jedwards4b/updateto258 0767c56bf Merge branch 'master' into updateto258 741f01b06 Merge pull request #1929 from jedwards4b/readonly_init_decomp 42463401c update pio version to 2.5.8 fe8526389 turn off doxygen build in test 2e9e8d659 Merge branch 'readonly_init_decomp' of github.com:jedwards4b/ParallelIO into readonly_init_decomp 3e832ff92 turn off doxygen warnings 02fa28809 remove halo in test b033009c9 remove halo in test 8315a9583 revert netcdf version 992d5970d add debug flags 793c83be6 try again d292334f9 try again 98b30a053 looking for mem leak 5bd5cfb0e initialize exp_val 295b5da30 testing memleak issue a25ef8105 more doxygen 4f206ecac update docs a9dc65d65 try this 1dd48891d cleanup fortran interface 216faa114 fix format bf342d0bb Merge branch 'master' into readonly_init_decomp 72d31a229 add new file to autoconf build da18105e6 add the pioc_async.c file 11df9a2ff Merge branch 'readonly_init_decomp' of github.com:jedwards4b/ParallelIO into readonly_init_decomp adb084450 add a test for initdecomp_readonly 0eb7ad638 copy back from ESMF develop cd9dae11a Add BUILD_SHARED_LIBS option c3c042e32 Merge pull request #1926 from climbfuji/feature/update_license_to_apache2 23153d5ba Replace COPYRIGHT file with LICENSE file in Makefile.am db104184d Remove old COPYRIGHT file f09ce7d09 Create LICENSE c5d622612 Merge remote-tracking branch 'mydev/startlist_err_fix' into readonly_init_decomp 9215ad2f7 remove debug print statement 10c08240e better fix de3bc6ff5 debugging workflow eeaa57f4b debugging workflow 6ce4184cf debugging workflow 5de7f424c debugging workflow f97ef84d1 fix an error in computing startlist and countlist for pnetcdf e3d835e1e an attempt to reduce memory consumption and improve performance d13e39116 Merge pull request #1924 from jedwards4b/move_to_heap 233c141bd move this allocation to the heap 6954d2f6f Merge pull request #1923 from jedwards4b/version_257 8986c3174 update version to 2.5.7 ec0878108 Merge pull request #1922 from jedwards4b/change_cmake_minimum 959dcfc6a closer to requred cmake minimum a91d94c12 Merge pull request #1921 from jedwards4b/parallel_sort 8e1220f16 undo debug change a95b5b602 fix conflicting types c0e367b20 fix conflicting types ff14c8f26 cleanup and debug 6cb1b45ca remove check for size of MPI_Offset 5bc2d18bd debug github workflow 92ad82b5a debug github workflow aae9abfd0 remove debug print 41ee148f1 cleanup cd2e3ff37 add a comment 6f36ec155 fix run_unique_check dedf05a53 only check readonly on compute tasks 8ea3ec589 add parallel_sort to autoconf build 83f1d1482 Merge branch 'master' into parallel_sort ef4bebd9d consider this change, not yet working 5cd4f369a Merge pull request #1920 from jedwards4b/update_cmake_minimum f12a7c603 fix compmaster test 2ae945860 fix compmaster test 7edc061ba fix communicator 38f85db2d need to check readonly for subset c913401f8 only add fortran dependencie if fortran build enabled 9141ce508 clean up testing 628a60805 update minimum cmake version, based on the oldest I can access a95907685 Merge pull request #1916 from jedwards4b/remove_MPI_Offset_redef f6faded05 remove the redefinition of MPI_Offset and MPI_OFFSET 0dbdf3b43 Merge pull request #1915 from jedwards4b/update_version_2.5.6 949c4acde update version to 2.5.6 f49656d57 Merge pull request #1911 from jedwards4b/subset_rearr_fix fbd8a0a54 a little cleanup 2f106a310 fix in esmf mesh read 907954dea improvement 36d85f710 fix for subset rearranger bug in 2.5.5 fa73d277e Merge pull request #1906 from jedwards4b/fix_netcdf_src_path_for_workflow e136d362c fix it again ebc8c9009 revert configure, test github caches - all workflows passing 2ca91d809 add hdf5 version and dependancy 98bb52f88 more github action fb8172f29 fix cache 1f242695b fix libpath maybe 8cf23ae93 backout 4.8.1 use 4.7.4 ada3d061b more netcdf download 87a2a1105 get netcdf from github not unidata site a755d3a38 get netcdf from github not unidata site ffaeefe93 update NC_DISPATCH_VERSION c75831cea fix line return issue 63e54ed05 all netcdf downloads now updated 255657ced add oversubscribe 3bb48a798 cut and paste b67943796 cut and paste 758e18665 reformat with yamllint d0978d431 reformat with yamllint 924b80d3f reformat with yamllint 4f1fe5f62 reformat with yamllint 936bc928f reformat with yamllint e6837b890 reformat with yamllint 1c2236b8f reformat with yamllint a03b0bfba try again a9ad7893b try again 9a26ba14a try again 4a65c35c6 update netcdf download path e352fd214 Merge pull request #1902 from jedwards4b/64bitdata 5e6aa9037 #define PIO_64BIT_DATA NC_64BIT_DATA requires netcdf 4.4.0 or newer f50f03872 Merge pull request #1899 from jedwards4b/add_write_nc_decomp_support_fortran 776de3e5c move these to a seperate repo b70ffd283 add the decomps using lfs 9737b204d add decomp files using git lfs d3a8ec8da Merge branch 'master' into add_write_nc_decomp_support_fortran bb253aba2 add pio_finalize call a4ed64c14 Merge pull request #1896 from jedwards4b/pio_buffer_size_limit_rename d8da2d2b3 Merge branch 'master' into pio_buffer_size_limit_rename 97ea899d7 Merge pull request #1897 from jedwards4b/fortran_deletefile_returncode 9576b8533 fix documentation 79b24b3c7 make fortran_order logical 469cfcba6 add fortran interface to nc dof read and write routines, add a translate program 8b45af91d begin add fortran support for this 58c45f968 document new parameter 10b733273 fortran pio_deletefile return code, optional for backward compatiblity 51524e5d7 rename pio_buffer_size_limit to pio_pnetcdf_buffer_size_limit c1307bf21 Merge pull request #1887 from NCAR/ejh_version 1175c39c9 Merge branch 'master' into ejh_version 0fb64ab47 Merge pull request #1891 from jedwards4b/refactor_subset_method 765557a91 Merge branch 'master' into refactor_subset_method 856fb305e remove cperf from tests 226dbe93f debug cleanup badc1c033 changes for serial build dbb3e5440 document new routines acc35223b document new variable da1cb8ce5 Merge pull request #1886 from jedwards4b/address_sanitize_patch ad2819e59 undo whitespace changes 1e50df7e0 undo whitespace changes d304db9b7 undo whitespace changes f249286e4 undo whitespace changes f95d648b4 cleaning up b48c44e62 Merge branch 'master' into address_sanitize_patch e99ffcb1c working for SUBSET rearranger b8bfef8e9 continued development of piodecomptest 0f3214a35 an attempt to refactor the subset rearrange method a1526a296 Merge branch 'master' into ejh_version 877986194 Merge pull request #1883 from jedwards4b/pio_byte_to_mpi_signed_char c6d90dd8f changed version to 2.5.5 870649ba5 fix bug in pioc_read_nc_decomp_int 0e3762da5 remove tabs from file 1e21296cc fix an issue exposed by address sanitiser 699c65187 remove travis test documentation 35a5339a8 remove travis test ecf94f315 update tests adding pnetcdf for BYTE and CHAR 982e77468 pio_byte type should be mpi_signed_char and not mpi_byte 468c06a59 Merge pull request #1881 from jedwards4b/cmake_fortran_cleanup 6d518a071 Merge branch 'master' into cmake_fortran_cleanup e4087a375 only do cmake fortran if building fortran interface 6ffa5d1b1 Merge pull request #1879 from jedwards4b/cray_compiler_fix 297c5d096 fix inconsistancy in intent 4dafb796e Merge pull request #1876 from NCAR/ejh_ranlib 4586f2cf8 fixed overflow in test e85dc3785 Merge pull request #1875 from NCAR/ejh_fix_dist 2c67ab15a add exampleAsyncPio.F90 to the autotools build fc1a67924 Merge pull request #1871 from kgerheiser/bugfix/macos-common-symbols 7e2e00a6c Merge branch 'master' into bugfix/macos-common-symbols 77a1ea044 Pass -c to ranlib to include common symbols on macOS 6d4bb2879 Merge pull request #1870 from NCAR/ejh_fix_dox_version b05b483c1 fixed version 0dc7d8ff8 Merge pull request #1869 from NCAR/ejh_release a2bd6367a updating versions 357ca506c Merge pull request #1864 from jedwards4b/check_netcdf_errfix 9a4e836ca try this 59ad3368c cmake still failing add debug code 0638adedf set WITH_MPIEXEC --oversubscribe 35c04b6fa set WITH_MPIEXEC --oversubscribe a06dfa2de add oversubscribe option 73716f7e4 try --oversubscribe d44762937 revert change to strict autotools workflow c9a944862 Merge branch 'check_netcdf_errfix' of github.com:jedwards4b/ParallelIO into check_netcdf_errfix 4fe2cd24f merge master for workflow fixes 550160bca Merge branch 'master' into check_netcdf_errfix 813e7c159 Merge pull request #1860 from NCAR/ejh_2 264242b58 refreshing caches d86865dee refreshing caches faebeea33 refreshing caches 6ea34b9e4 refreshing caches 03ff8f545 remove enabled-shared pnetcdf option 8d44884f3 try fix for pnetcdf fac7ee7dd fix error in check_netcdf call and in detecting dap 612014640 Merge branch 'master' into ejh_2 0ec340c76 Merge pull request #1859 from NCAR/ejh_versions c67d8c279 resetting caches 1b901c0db triggering CI 2bab8b463 one more try 7accbbad3 updated version numbers for release of 2.5.3 53497cafb Merge pull request #1857 from jedwards4b/pnetcdf_support_cmake 6f0b9bf16 fix indicator for pnetcdf support in cmake c77a30d95 Merge pull request #1855 from jedwards4b/create_logfile_only_if_loglevel 983bd8e66 only create log files if log level > 0 989e026f5 Merge pull request #1854 from jedwards4b/redef_from_def_test 7df2e2afe remove this test, no longer valid 360a360ac Merge pull request #1852 from NCAR/ejh_readme af9b0733a commented out test_async_1d ca842d15a commented out test_async_1d 66132141f updating readme 5206ff4c5 updating readme c6fd1755c updating readme 47f466fd1 updating readme 8b2f798a4 Merge pull request #1851 from NCAR/ejh_cmake 4ea3f9362 turning on netcdf integration in cmake build 304b7296e Merge pull request #1850 from NCAR/ejh_next_1 2123df499 turned test code back on 40d9637c2 Merge pull request #1849 from NCAR/ejh_next 582d6f7b6 turned test code back off 0a41fbf89 turned test code back off d7eb8207b turned test code back on 41ac8bc7f turned test code back on 2f90688c7 turned test code back on 9f6b1b5c9 fixed type size in async code 16b469d00 turning test code back on 268c69929 Merge pull request #1848 from NCAR/ejh_preprocessor 558f24000 cleanup of automake and pre-processor symbols e8a87005b removed pre-processor symbol USE_NETCDF4 77a31b1bc Merge pull request #1844 from NCAR/ejh_no_pnetcdf_build 818eead20 commented out part of tst_async_multi 7b0b78b16 commented out part of tst_async_multi 41ea01e99 commented out part of tst_pio_async 388681f92 commented out part of test_async_1d 34f6b99db fixed no-pnetcdf workflow, renamed ubuntu latest workflow 463e37d4e adding new workflow dddf14773 Merge pull request #1843 from NCAR/ejh_warn c95152b6e fixed warnings and netcdf-integration build without pnetcdf 2d0c61c2e Merge pull request #1840 from NCAR/ejh_cmake_again_3 444c30dc4 fixing cmake workflow b43e67e44 fixing cmake workflow 42366fb63 Merge pull request #1836 from NCAR/ejh_cmake_again dcaba92f8 changed test timeout in cmake 19570c281 fixed code warning, removed print statements from test f632317cd make configure search for netcdf-fortran if --enable-fortran and --enable-netcdf-integration are used 57446873a debug test 9b5964267 add fortran build c6912419b fix paths 3705bbdf2 adding fortran f65e972e4 adding fortran d914a8353 adding cmake build 9accccb00 Merge pull request #1835 from NCAR/ejh_cmake_fortran_workflow 27d20a3be try a different cmake? ee9fe1b61 giving up on cmake build for now ebfb0e503 adding another cmake build 8fd204e80 adding another cmake build 219d72fb9 adding another cmake build ed0304884 turned off fortran in cmake build b56162ef1 fixed fortran test 5c34c279f turning on fortran build in cmake workflow ee329568b Merge pull request #1833 from NCAR/ejh_ncint_test_2 85f50f29d more testing da6015c2c Merge pull request #1831 from NCAR/ejh_ncint_test 11959c931 fixing ncint test for 4.7.4 by commenting out code 8dbde41a0 fixed comment ccbb2302f fix test_darray_multivar3.c 7172df901 turning on netcdf integration in workflow e53623410 Merge pull request #1826 from NCAR/ejh_test_more 1eb5a219d working on workflows 40ce8ea26 switching to pnetcdf-1.12.2 593e85371 adding testing 0f0558ffe adding testing 0f3502fa0 adding testing 862538461 Merge pull request #1823 from NCAR/ejh_more_tests 71a695cba working on asan build 70066f238 working on asan build b5801cd8b working on asan build 8fd651963 working on asan build a679c5bd5 adding testing with hdf5-1.10.7 3308d5e93 renamed workflow files to reduce confusion f34ef23a9 merged master 0887324d4 fixed warnings, trying to get asan workflow to build 6947e3114 Merge branch 'master' into ejh_more_tests d862880a7 added asan testing e341609e3 Merge pull request #1821 from NCAR/ejh_test_on 1464bf0a4 Merge branch 'master' into ejh_test_on ef34338ae fixed test_darray_multivar3.c 2d6de331b fixed test_darray_multivar3.c 1ef9493f0 Merge pull request #1820 from NCAR/ejh_default_blocksize 9e492a483 changed default blocksize 36eba03fa Merge pull request #1817 from NCAR/ejh_docs c7b3010cc documentation improvements 082fc0f32 documentation improvements cacb65e7b documentation improvements 9548daac5 fixed warnings in code 4200f55a1 Merge pull request #1809 from NCAR/ejh_perf_more ce23930d6 now setting chunksizes for netcdf4 performance runs f59373773 whitespace cleanup 6f7a1dcdf fixed mpe problem in test_simple.c 9a669de89 modification to perf program output 9abd0ca71 Merge pull request #1806 from NCAR/ejh_perf 329ef8f2d cleanup 9f912f859 merged master be3b13f22 fixes to test_perf2.c 84511247c Merge pull request #1805 from NCAR/ejh_fix_test 5df3c5dc6 whitespace cleanup 118e44a76 better async error handling in tests 57c03b9c3 whitespace cleanup 379983a92 more fixes for async test error handling 9bdf340a2 more work on async error handling 25d5bf4f0 more work on async error handling 3b550c794 more work on async error handling f83540176 more work on async error handling bb6adea7f fixed comment b44d3237c better handling for test failure in async tests 40da636a3 added AERR() macro for errors on async tests d8ec81a98 fixed comment 9cec790f1 fixed whitespace issues in pio_error.h d14471895 fix printing of some incorrect error codes in cunit tests 9dad4e97a Merge pull request #1802 from jedwards4b/avoid_msg_starving e6fc3e00b clean up test 90f497c14 change waitany to waitsome to avoid message starving 53bdadcbf Merge pull request #1800 from NCAR/ejh_docs_2 dd1b8d038 updated documentation and cleaned unneeded preprocessor symbols from test_perf2 and test_async_perf 5d0f8a5b0 Merge pull request #1799 from NCAR/ejh_t1 eec9e0b50 stop running test_async_perf with other CMakeList.txt tests c254d12f0 turned off logging in test e86c55cb6 try reducing the size of this test 358e71917 document new error code b51b8324c move large allocate from stack 4f01bc28b fix test 570abae1e add error for rearranger mismatch in async mode 564a15116 fix async_perf test 860f6f99f Merge branch 'more_async_tests' of github.com:jedwards4b/ParallelIO into more_async_tests a8493e337 add test_async_perf to cmake build 66564a550 Merge branch 'master' into more_async_tests 5852d9093 Merge pull request #1765 from t-brown/master 40da5e29c add SUBSET rearranger d741f3700 Merge branch 'master' into master 1a3fa8630 Merge pull request #1794 from NCAR/ejh_fix_perf 2184073b0 Merge branch 'master' into master 2a2a08dad turned off subset rearrarger in test_async_perf b51f6768c more improvements to performance programs 6a29e16eb merged master f0a9c0ad1 fixing test_async_perf 5ca0b5586 Merge pull request #1791 from jedwards4b/async_subset 6b08ffb66 now test both rearrangers in tst_perf2 d956b7904 added commas to output 7e385d133 fix test bbe58daf7 add tests c8f91fbca subset working in async 744b73163 Merge pull request #1790 from jedwards4b/add_nf_pio bbb9ed716 remove need for netcdf or pnetcdf fortran libs 53d652ed8 add netcdf fortran build 5d1ca6791 add nf_pio, netcdf now defines cdf5 format 8a0cb4f84 Merge pull request #1786 from jedwards4b/sort_only_on_compute 3d49f3008 array sort should only happen on compute tasks 7f28489f5 Merge pull request #1784 from jedwards4b/add_async_get_att_test 4b79b0203 add new function to include file 15921d6ff fix documentation biff d937cc331 add global_set_log_level, fix issue 5cd85396f add async test for get_att - test currently timesout 38d9acda5 Merge pull request #1782 from jedwards4b/async_fixes ffe4098c1 move malloc to correct location e05d8f2b0 remove unneeded change 7806081b4 changes for async interface 7e242f78b Merge pull request #1781 from jedwards4b/with_pnetcdf_cmake 6c4d85875 use WITH_PNETCDF in CMake build f960b3799 Merge branch 'master' into master 1d0dabdf3 Merge pull request #1778 from jedwards4b/add_pio_init_async_from_comms 1de5ded13 Merge branch 'add_pio_init_async_from_comms' of github.com:jedwards4b/ParallelIO into add_pio_init_async_from_comms 7a52d1d9d try this 875966b5b fix mem issue 60f9f17f3 fix documentation f63773317 remove .f90.in from gitignore file, add tests cf09cd22d remove unused var 7f28e28cf fix Makefile.am 8af4d74d9 try again 2d3cb219a fix test generation issue 4a012a898 add test to autoconf 155c11dee fix line length issue 01e9e31dd add async test from fortran bcc711331 remove set_log_level from test 8f10a32a2 remove debug print ea404f6b3 add PIOc_init_async_from_comms and test 53c5a2c23 Merge pull request #1776 from jedwards4b/update_f_examples 0f5da9dc3 Merge branch 'master' into update_f_examples a8acfd49d more doc cleanup cad018af7 more documentation and refinment 4fd48cfce add some documentation 9e999911c correct ranks in async 0f65ecc0d cleanup a27009b57 working example from fortran 81c778517 Merge pull request #1774 from jedwards4b/unique_name_err_buffer e079cb408 make example resultlen distinct names from that in pio_error.h c30ff49c5 make example err_buffers distinct names from that in pio_error.h e26c200c2 work on async interface 092a618ee begin work on fortran async interface 66449308c Merge branch 'master' into master 7309b9b60 Merge pull request #1772 from jedwards4b/more_fortran_interface c59a6d644 remove bad assumption 0a565e497 more fortran interface changes 2d4202846 remove debug print c9e5d01aa fix nfget 74afc2a9a cleanup c7813144d fix test var io from fortran 1caa8c15c add pio_fill 134c5209d Merge pull request #1771 from jedwards4b/fortran_interface_updates c91eb59c0 back out setting of fillvalue in pio_darray f3b63c9cc untabify 01830e4eb fix whitespace 5ae954910 try again 94ff81b6a undo last change and see if travisci will pass 91520c20c read_darray sets fillvalue 736c0745c add target attribute 7bd521922 more minor changes 0ba4b787d implement pio_inq_var_fill in fortran, add tests e7d621b0b Merge pull request #1769 from jedwards4b/cdash_test_fixes 3eac73356 undo unessasary change 3d8956df3 fix pgi version and openmpi test error fed328b7c Merge pull request #1767 from jedwards4b/update_cheyenne_tests e47b8f108 update cheyenne modules for ctest 364a445bf Adding an autoconf check for C99. c90a7a287 Merge pull request #1761 from jedwards4b/remove_pio_use_malloc 3e432479a untabify c files b7b9b52e1 untabify pio_darray.c 9fc01568a Merge branch 'master' into remove_pio_use_malloc b241756e7 Merge pull request #1763 from jedwards4b/fix_int_overflow 1c9dd2823 fix integer overflow issue noted in nag compiler 9d3470f5e fix doc generation error 34809b99a fully remove pio_use_malloc macro b9855cdb5 Merge pull request #1759 from jedwards4b/add_flib_set_fill 78d28a329 add set_fill to fortran interface 6f9fb5e1b Merge pull request #1754 from NCAR/ejh_release 9efeee459 changed version numbers and so library numbers fd8b8c111 Merge pull request #1753 from NCAR/ejh_no_compress 00104f88b no longer turn on deflate for vars automatically d0d4a98f8 Merge pull request #1752 from NCAR/ejh_bget d048ed581 working on cmake test build cbf9b1728 working on cmake test build 4c545508b merged 14672d4d0 working on cmake test build a98bf4a15 Merge branch 'master' into ejh_bget 14ba34643 Merge pull request #1751 from NCAR/ejh_docs 668bdd323 more bget fixes c9923271a added cmake to test build bad9cee8c removed bget 2f3ed1128 removed bget d23ae965a more fortran doc work d751d495d improving fortran docs e97f23923 improving fortran docs 3a77973ad Merge pull request #1747 from NCAR/ejh_ncint_deflate 73eaa0c70 added endianness f97e66681 now testind def_var_endian 9c88c0eb8 now properly getting chunksizes thru ncint c298e796f developing test 09dc75601 added deflate to the test 58533898a modifying tst_var_compress f11724cc0 added tst_var_compress.c 39b0940bd merged master 64cdf4bdb Merge pull request #1746 from NCAR/ejh_mpi_check 286f52932 removed cmake build from github testing c2492f10a dealing with der_var_endian and def_var_chunking in netcdf integration layer 245a21257 adding PIO_NCINT_def_var_deflate b25c930d2 added check for MPI c5696275e Merge pull request #1743 from NCAR/ejh_more_tests_2 261d8b6fe increased time-out c6c613863 added cmake build to a4.yml adbb0d801 removed flags from fortran cmake build 63662f583 Merge pull request #1742 from NCAR/ejh_flags 666731d02 removed unused VARN pre-processor defines 3ce5db5d2 Merge pull request #1741 from NCAR/ejh_more_testing_2 81de16eab adding Fortran to build summary 6ec562a44 MPIEXEC in examples/f03 directory, also set FC in fortran build e835926b6 turning on fortran build in github CI, also fixing mpiexec in tests/performance a5fb922e0 handle mpiexec for fncint and general dirs 9e4a39ecb trying to get gcc version 3c02032ff Merge pull request #1738 from NCAR/ejh_more_testing eb23c9f03 fixing order of chunksizes 15a191b55 fixing order of chunksizes e37d19ae2 fixed chunksizes type size error in F90 api 13cb7c7fe fixed shell script with new test name f1e58bd7f renamed test 5ff984444 fixed docs 5c2ae6522 adding pio_inq_var_chunking 66754676c more test development f114fbc32 further test development a54de425a further test development cbed9880c further test development cdc01a165 turn of netcdf integration in github workflow 05ce8e39b added ftst_vars.F90 to CMake build 9d3ff03fa added ftst_vars.F90 to CMake build e9f4f755d starting to add ftst_vars.F90 2987785d5 turning on ncint f6feb76b1 Merge pull request #1737 from NCAR/ejh_flags_next 5f8e9fa71 more testing in new workflow 71eace1ca more testing in new workflow c2919cb03 more testing in new workflow 87e38c547 more testing in new workflow dd0400c9b more testing in new workflow 1733a7a48 adding mpich workflow a31c6f8e0 adding mpich workflow 138f4f14a adding mpich workflow d677d0765 adding mpich workflow 28429a54c fixing MPIEXEC in library summary for CMake builds 22d11602a Merge pull request #1735 from NCAR/ejh_cmake f130a86da adding fields to build summary f835a8d7f removing unneeded logging pre-processor macro from CMake build 9d8c81a61 clean up 1b788c9b7 more fixing for flib and clib, now fixing _PNETCDF e6960d9a9 more fixing for flib and clib 1bb4b5749 now fixing for flib 510e955f1 fixing CMake determination of _NETCDF4 843f6d906 commented out more unneeded flag setting in cmake adf6308d1 commented out more unneeded flag setting in cmake 6d767b2b1 commented out more unneeded flag setting in cmake d37b976bd taking away flag from CMake build 54ee841cc Merge pull request #1734 from NCAR/ejh_doc_fix 35742c688 now ncint tests repect WITH_MPIEXEC 151affd85 now ncint tests repect WITH_MPIEXEC 181373a76 fixing docs, cleanup of test workflow e715d0778 Merge pull request #1733 from NCAR/ejh_openmpi_2 7b874db3a clean up 7ddbfe753 trying to deal with MPIEXEC in CMake 41b1588a4 trying to deal with MPIEXEC in CMake 280c4b9ae trying to deal with MPIEXEC in CMake b501e625d trying to deal with MPIEXEC in CMake 7bcf9f33e trying to deal with MPIEXEC in CMake f5906b12e trying to deal with MPIEXEC in CMake 672259c4f trying to deal with MPIEXEC in CMake 48157639e trying to deal with MPIEXEC in CMake ba379cc66 trying to deal with MPIEXEC in CMake 2138bd3e6 trying to deal with MPIEXEC in CMake b2820c2c6 trying to deal with MPIEXEC in CMake e80292528 trying to deal with MPIEXEC in CMake b1fabeea1 trying to deal with MPIEXEC in CMake 4174cf9a4 trying to deal with MPIEXEC in CMake 74223248a trying to deal with MPIEXEC in CMake deed51058 trying to deal with MPIEXEC in CMake d561d64c0 trying to deal with MPIEXEC in CMake c0466f9ac more work on cmake build 6eb1b7a25 more cmake build 1ac66e0e0 more cmake build 51791cba4 more cmake build fc04c721a more cmake build afb423be5 more cmake build ddb380f70 more cmake build 9e654d80a more cmake build 4c1ca9eb9 more cmake build feada9c08 more cmake build f2bbbbf9c more cmake build e23ce03d6 more cmake build 101381853 more cmake build 081b86327 more cmake build 36b7c7bae more cmake build f38d8ae16 more cmake build c16d88a5c more cmake build 7f547ee06 starting to add cmake build of C library 00e667f64 Merge pull request #1731 from NCAR/ejh_openmpi 0f2db9d11 converting more tests to use new --with-mpiexec option c7fc47aac converting more tests to use new --with-mpiexec option dc8275df5 converting more tests to use new --with-mpiexec option 2af2aeb4f adding tests/cunit/run_tests.sh.in db613c3e5 adding tests/cunit/run_tests.sh.in e4fb33c03 adding --with-mpiexec option to configure 2d908a13a adding --with-mpiexec option to configure d76dd49b6 trying to get openmpi mpiexec working 3822956e3 trying to get openmpi mpiexec working 558a3b9c4 trying to get openmpi mpiexec working ba2b71983 trying to get openmpi mpiexec working 493353ae8 trying to get openmpi mpiexec working dcb5e0807 trying to get openmpi mpiexec working a96671fd6 trying to get openmpi mpiexec working f283a8030 trying to get openmpi mpiexec working 0903e6223 trying to get openmpi mpiexec working 5a96af866 trying to get openmpi mpiexec working 2d9bf6b69 adding PIO b35ee2110 adding PIO 2bf634f90 adding PIO cc1dc81ab adding PIO 8b243ca4c adding PIO 3681f56be adding PIO 0c5dbbd37 adding PIO 11203423d adding PIO 8984b2654 adding PIO 7a5c3f306 adding PIO 8f865959e adding PIO 4d1a70939 adding PIO 61ef8dede adding netcdf-fortran and pnetcdf 6d2b2a9aa adding netcdf-fortran and pnetcdf 35dda9d5b adding netcdf-fortran and pnetcdf 49ab2d773 adding netcdf-c 1199dd36c adding HDF5 1c5ab7603 adding HDF5 ae45f2bf9 adding HDF5 ab7782790 adding HDF5 dc6eb09b9 adding HDF5 2b766e2d2 fixing apt-get for curl 5d9b54b65 building openmpi 0697d04d8 building openmpi 0043527ad Merge pull request #1725 from NCAR/ejh_next_9 41b62fb6f fixed warning, turned of -Werror for fortran to try and get github workflow building c76f148b7 fixed warning, turned of -Werror for fortran to try and get github workflow building 32640e6f5 fixed warning, turned of -Werror for fortran to try and get github workflow building 3b6387898 fixed warning, turned of -Werror for fortran to try and get github workflow building fb4052a00 turning on -Wall for strict autotools build aa9f62cfa turning on -Wall for strict autotools build 1085b9521 Merge branch 'master' into ejh_next_9 23c5c50df Merge pull request #1726 from jedwards4b/reduce_search_netcdf 43f131525 remove more redundant find_package calls 6526724a8 add space cc11af948 no netcdf fortran in this test 8b97bd5b0 remove debug print statements 57f939fdf only search for netcdf at top level fe2fb7a7b removed extra workflow for now 5acda4b96 error out of cmake if netcdf-c dispatch table wont work for netcdf integration 52367bd73 trying to add another workflow a043a91fd trying to add another workflow 9be18aed4 took comments out of workflow file b26239d50 adding netCDF interation to build summary and pio_meta.h f1a83f3c1 Merge pull request #1715 from NCAR/ejh_ncint e57c5aa1c properly dealing with ncint_mod.F90 in cmake build 78dd092ef clean up 15527bf8e cleaned up cmake_config.h.in a604f76f3 added new github workflow for netCDF integration with cmake 08c7999e2 now all ncint tests work 444f0233d more work on ncint in cmake build 6bd5fa473 moved cmake build of ncint into src/clib dir, now test works! 9f57a5cc5 ncint build working! eaa065607 now building ncint directory with cmake cab47c393 merged changes from master a59a55b19 Merge pull request #1722 from NCAR/ejh_next_7 a1a04ef2e moved .f90 to .F90 089a7ecc6 turning off logging in a test 5b7f80104 more fortran flag cleanup 5f190e84e more fortran flag cleanup 7067c6331 cleanup of flags in test/unit autotools build 4d6e4f864 more flag cleanup a91eed922 more flag cleanup db93ea51b more changes so that all fortran files use config.h 0a10f86bc adding some cmakedefines 6213867ab cleanup of flag use in src/flib 4f80a53a9 Merge pull request #1720 from NCAR/ejh_next_6 0b2bebe4b removed unneeded pre-processor symbol from cmake_config.h.in 9b942c5bf Merge pull request #1719 from NCAR/ejh_next_5 b258478c3 removed troublesome strnlen() function 85edfb827 removed more unneeded pre-processor stuff 1ac844fff removed more unneeded pre-processor stuff 8a82deae2 removed more unneeded pre-processor stuff 8a8ba30d3 more removal of unneeded pre-processor symbols 4754ab5f4 removed unneeded check of _NETCDF ad4eddb75 removed NETCDF flag c99eb2896 Merge pull request #1718 from NCAR/ejh_next_3 4430bcd2c changed build summary 2676343e7 clean up travis file 7153ec973 removed constant 084f1c18c Merge pull request #1716 from NCAR/ejh_next 90d9af625 removed config constant that is unused anywhere... f269769d9 fixed setting of configure define in cmake b38aaefb2 starting to add ncint code to cmake build a28ec8c22 fixing cmake use of defines c5794a848 trying to fix cmake build 768c0c4a6 merged master a9ed7f1d4 Merge pull request #1714 from NCAR/ejh_fix_cmake_2 b9855320d fixed creation of config.h on read-only filesystem 52ac327ff adding support for NETCDF_INTEGRATION option to cmake, also fixing cmake build issue in read-only directories 116cd6eb1 Merge pull request #1710 from NCAR/ejh_cmake_fix 03006885f including HAVE_PAR_FILTERS in cmake config.h eed7d4886 Merge pull request #1707 from NCAR/ejh_cache_2 c0aa71a63 now trying caching for cmake build fc96bb3cf now trying caching for cmake build 6d93e738d now trying caching for cmake build 359bc447a now trying caching for cmake build 9b46b90e1 now trying caching for cmake build e307f964e now trying caching for strict pnetcdf build ab5f23485 now trying caching for pnetcdf build 7e4002993 now trying caching for pnetcdf build e11337c10 now install pnetcdf in subdirectory 23766326c Merge pull request #1705 from NCAR/ejh_fix_makefile 658b209b4 fixed makefile 9d4dbb773 Merge pull request #1700 from NCAR/ejh_4_7_2 ce1828aae took out caching attempt 09a7b2cf9 added comment bb3fc1423 cmake determination of par filters presence 5e5132326 attempting to cache pnetcdf build in workflow 348294616 changed fortran test to ignore deflate tests on NETCDF4P iotype f591b8c22 now use HAVE_PAR_FILTERS in test_pioc.c 8a298dca3 now check for netcdf-c disptach version in autoconf and cmake f66d558c6 fixed detection of 4.7.2 in autoconf to work for old netcdf releases that don't have netcdf_meta.h 042ea8157 added nc-config output to travis 3f4504890 added nc-config output to travis e049af45b added nc-config output to travis 8ac93feb5 added nc-config output to travis 783ff4d29 added nc-config output to travis 4ed861e07 added nc-config output to travis e0eb09028 disallow netcdf-c-4.7.2 for both cmake and autotools builds a14b65b3d Merge pull request #1698 from NCAR/ejh_test_simple ee339d016 fixed cmake running on 4 procs 62d09eecf called MPI_Finalize() in test_simple.c 8f40a3ae1 cleaned up simple test 39d4c796b merged master eedc46cd1 Merge pull request #1696 from NCAR/ejh_fix_test_leak 4438bf5a7 turns out we need fortran for pnetcdf 28fcb4852 turn off cxx and fortran for pnetcdf build 56243cfc0 turn off netcdf-integration in travis testing 88cf3d137 turn on netcdf-integration in travis testing abef381ae fixed memory leaks in tests 64a117c58 Merge pull request #1690 from NCAR/ejh_docs_2 e663bf300 removing redundant build 05ad86b24 turning on fortran build for autotools 90a1a2076 turning on fortran build for autotools 087658592 turning on fortran build for autotools dd9d7ddc7 trying doc build a different way 0cdc421a5 trying doc build a different way 0e6e349ea trying doc build a different way 602f71c6d Merge pull request #1688 from NCAR/ejh_more_summary 3601aeab0 clean up 0ff7f7b03 added new feature settings to pio_meta.h 090012657 added netCDF-4 and netcdf-4 par to list of features in summary dfc908e5b Merge pull request #1685 from NCAR/ejh_fix_summary 97890481e updated summary cdb24f5af fixed libpio for autotools builds with fortran info, added FCFLAGS 903fc75fb Merge pull request #1683 from NCAR/ejh_cmake_2 addb05c0c adding cmake build 7074cf973 adding cmake build 2928d62fe adding cmake build 94efbbea7 adding cmake build 6da9b1162 adding cmake build 7b2f0d1df Merge pull request #1680 from NCAR/ejh_fix_test 3f10bbc82 ok, dial back on docs for now 4ed34f506 ok, dial back on docs for now 17c71cf04 Merge branch 'master' into ejh_fix_test cb4ea896e Merge pull request #1673 from jedwards4b/jedwards/cmake_piolibsettings e773963b4 still trying docs f5150086b now trying docs as well ef28e9bd0 now trying docs as well 047e55765 Merge branch 'master' into jedwards/cmake_piolibsettings 353031d0d trying to get env vars working f501ad216 fixed yml error 8e011fc2e change to trigger CI aa8bdb5dc change to trigger CI 72186bb1b Merge pull request #1679 from NCAR/ejh_add_strict_workflow 253eb9046 commented out running of test_darray_multivar3.c fbf9c3ab4 commented out running of test_darray_multivar3.c c856445d1 Merge branch 'master' into ejh_add_strict_workflow a23f25662 commented out running of test_darray_multivar3.c 1c7040604 Merge branch 'master' into jedwards/cmake_piolibsettings 6400614d5 one more fix d51d7b963 additional output from cmake 391f72032 Merge pull request #1671 from jedwards4b/jedwards/rec_var_fix aec3413ff uncommenting much of the commented code in test_darray_multivar3 11a9ad571 cleanup, update pnetcdf lib 79b4b026a try again 531882a46 add space 266e0403c append not prepend 41dc2c96c removed extra make invokation 34059c62a turned on asan for C aabe4ec82 try again 3e5dd3d31 turned off asan 96b25f96b try updating travis script 1dd31fd48 adding strict autotools github actions workflow ca3b8c24c add test to Makefile.am 39d9ae1c3 dont compare what you dont know df2c37a9d Merge branch 'jedwards/cmake_piolibsettings' of github.com:jedwards4b/ParallelIO into jedwards/cmake_piolibsettings e66c8f457 add debug print for travis 5e2a76f0b add a test 03335fff9 remove PLOG 8d293ab1c Merge branch 'jedwards/rec_var_fix' of github.com:jedwards4b/ParallelIO into jedwards/rec_var_fix 9bc0a8a02 conditional plog 1e3330a11 Merge branch 'master' into jedwards/rec_var_fix fb0d63d9e Merge branch 'master' into jedwards/cmake_piolibsettings 5d3d0ff7c Merge pull request #1674 from NCAR/ejh_test_ci_2 0c1d34364 renamed builds to avoid confusion 73d2b8b69 removed extra build to avoid confusion 0b92d3b52 change to trigger CI dda3ba492 backout change for travis test 5dc5719cd improve libpio settings output from cmake f6ad7c593 fix initialization of var rec_var 2bd7f60b4 Merge pull request #1668 from NCAR/edwardhartnett-patch-2 3b6bbe32a Create master_netcdf.yml 282e3381c now can turn on deflate with netcdf-4 parallel e7cdd55ce got working for current state of play 3d4b09eab now reading and checking data aee02f360 getting test_simple working a430197eb getting test_simple working 09965b853 added unlimited dim, also creating decomp 137db078f now creating dim and var in test_simple 0c1589224 starting to fill in test_simple 56ea154d0 developing simple test 958d9b91a added test_simple.c 53b2a79e6 Merge pull request #1666 from NCAR/ejh_error f2a2e6359 added pio_error.c to Makefile.am 9816c7e5d merged in bugfix/gcc10-multiple-definitions e6d4a15d4 Merge pull request #1665 from NCAR/ejh_pio_next e4f5c0191 fixed comments 2ad546c70 fixed version in cmake output of pio_meta.h 5246b64e7 fixing szip write flag again! 9224d770c fixing version numbers again! 8444d383f fixing version in cmake builds b90d6c527 change for CI d64a09afe Reorder dependencies and add pioc for pio_tutil target cfb02eb71 Fix parallel build failures for make check by adding dependencies and compiling fortran modules only once. 1533e32fe Add missing headers 893b2de6f Fix multiple definition errors with GCC>=10.1.0 by seperating definitions from declarations c8a0245fe Merge pull request #1659 from NCAR/ejh_summary 2f3daaf72 Merge branch 'master' into ejh_summary c3e2839bb Merge pull request #1661 from NCAR/ejh_actions 145456080 working on GitHub actions build 5244094b6 Merge pull request #1660 from NCAR/edwardhartnett-patch-1 38ca1b0c1 Create c-cpp.yml 804e05a15 getting pio_meta.h working in CMake d8bff5c95 add pio_meta.h.in 87bf3fda7 add pio_meta.h.in f536ece91 add pio_meta.h.in 9fce7ef11 add pio_meta.h.in 3c6b51d65 more work on build summary 24a6b6bc4 working on build summary 25923f350 further development of build summary da613e596 adding libpio.settings.in cdf9704b2 added *.F90.in to gitignore 9316d5cc7 add libpio.settings.in cb5342dc6 Merge pull request #1657 from NCAR/ejh_25 4445b0f05 fixed cmake version number ba330d4ec updated version numbers aeefa825f Merge pull request #1656 from NCAR/ejh_doc_fixes 69e4178c4 updated docs with feeback from Jim 7bc20b4ba fixed documentation errors 35b513ee0 fixed documentation errors 58e255c8f Merge pull request #1655 from NCAR/ejh_release 599e32fdd updated libtool release numbers e1fa7f7f3 changed version numbers 1ff0f440a Merge pull request #1653 from jedwards4b/short_type_in_fortran b0890739a Merge branch 'master' into short_type_in_fortran 30a1b792d Merge pull request #1650 from NCAR/ejh_fix_warnings_2 1c448afc8 fix mem error 038b3a7e8 Correct -D_PNETCDF flag 14140f871 revert travis b78ee9747 bionic didnt work try Xenial 750209f1b try updating travis build f44b71e40 update genf90 external 01452c3b0 add short data type to fortran interface and tests b049420c8 add a short datatype to the fortran interface ceff4ea21 fixed warnings in tests a4fb42f0a Merge pull request #1644 from NCAR/ejh_netcdf_4_7_4_more 82e781cd4 changed test to always use deflate of 1 20c529c25 Merge pull request #1643 from NCAR/ejh_netcdf_4_7_4 e722b8119 turned off logging in test ed7c53a3a restored test 8365a2c6c no longer try to set deflate on scalar vars f8a327558 adjusted dispatch table for netcdf-c-4.7.4 e41e6a652 Merge pull request #1638 from jedwards4b/logging_bug_fix 92418ee9f if rindex is null and debug is enabled this will segfault 6aa9c6038 Merge pull request #1634 from NCAR/ejh_warnings cac94b3c0 removed unneeded initialization of vars 1a3799db3 fixed warnings related to netcdf integration code d92cb2801 Merge pull request #1628 from NCAR/ejh_fix_alloc 7114c751d moved decl for performance 72c5bd5b2 Merge pull request #1622 from NCAR/ejh_perf_4 341c123ff fixed up test program 6ddc1a024 split async perf test out a8f7076ef Merge pull request #1620 from NCAR/ejh_ncint_perf_3 e5708e1f4 fixed table output 85f67f990 more development of performance program b16e033d3 testing different iotypes in performance test 6c03fdbb5 Merge pull request #1619 from NCAR/ejh_ncint_perf_2 b59669578 improvements in performance program b9b900b1a Merge pull request #1618 from NCAR/ejh_ncint_perf 65bef9b2f no longer automataically deflate vars for IOTYPE_PIO_NETCDF4C if opened through netcdf integration a8ea44c90 ncint performance test 751ff3d1c Merge pull request #1614 from NCAR/ejh_prepare ade6fb545 fixed header files b1510169e changed version numbers 8c3ab430c Merge pull request #1611 from NCAR/ejh_dos 1376df147 fixed docs in pio.h 932fbdb25 fixed docs in pio.h 824f576fd Merge pull request #1610 from NCAR/ejh_includes_2 8d283f283 removed more inappropriate ifdefs from pio.h 12209c7a5 Merge pull request #1609 from NCAR/ejh_header cbcc78567 moving reliance on ifdefs out of pio.h c0079f600 moving reliance on ifdefs out of pio.h db7238801 Merge pull request #1605 from ckhroulev/cmake-install-uthash af26e0d86 Merge branch 'master' into cmake-install-uthash 2f1436add Merge pull request #1606 from ckhroulev/PIOc_InitDecomp_bc-off-by-one-bugfix 648109a52 Fix an off-by-one error in PIOc_InitDecomp_bc() 695809503 Install uthash.h when building ParallelIO using CMake b1b1fa7fb Merge pull request #1603 from NCAR/ejh_multi_ncint_async a8b8a42af only send iosysid for create/open when netcdf integration is in use 0d6cbc756 now netcdf integration works with multiple computational components with async f19543590 now passing diosysid when doing a create file in async mode 85ec39cd8 fixed ncid issue for PIO opening second file d6097d97f moving code to function so that multiple computation units can be handled 94cdb68ee moving code to function so that multiple computation units can be handled fc920975e adding new ncint async test b8db4c93f Merge pull request #1602 from NCAR/ejh_docs 85c15c290 version 1 of netcdf integration documentation 4664ac57e Merge pull request #1601 from NCAR/ejh_read_darray 5774d8141 fixed netcdf integration tests with read_darray() d6537da15 now testing read_darray() 16c8bfe32 minor changes 9c7f67cb5 merged master 49ab208a2 Merge pull request #1600 from NCAR/ejh_remove_ndims_call f07cbeca3 now store ndims in var_desc_t and no longer need to look it up in read_darray() 0020927f4 adding ndims to var_desc_t 9c4257dfb continuing to add ndims to var_desc_t 3d941c9ac dealing with allocation for ndims array 204ec0fb9 made inq_file_metadata a static function 4f579cf59 comments 7c2c7e74c more progress towards read_darray 14320d5c7 more progress towards read_darray f34f7b188 read_darray seeming to work, but cleanup of resources fails 11f62119b implementing async read_darray() 344b083d0 merged warning fix from master b53c2d3aa Merge pull request #1597 from NCAR/ejh_warning cf5173afe fixed warning 166b9afec beginning to implement read_darray for async ee94d4783 Merge pull request #1595 from NCAR/ejh_more_ncint 76405781e protect test_async_1d from classic only builds 564452b8c more test development 9633f7fa8 more test development 1503141de added test to cmake build 5eaa61d31 more test in test_async_1d 9682bb265 more test code for test_async_1d.c e6b40bcb1 adding code to new test test_async_1d 2c57b592f starting to add new test_async_1d 3686e8b2f starting to add PIOc calls to test 5ff9c23b4 checking more of test file 4b867994a checking more of test file 43c675159 checking more of test file 6012ed3d0 starting to check test file 20a3b29cc getting close to turning on int reads 3d8167a47 now testing open with netcdf integration and async 4a2a867ff proper handling of ncid in openfile_retry for async netcdf integration 3bd30e8af now calling nc_open when use_ext_ncid is true in open_file_handler() e1f1c88c0 now pass use_ext_ncid to open_file_handler() in pio_msg.c 5f46649ee more of async PIO test 1d55692d5 turned on more test 4b074a5e5 Merge pull request #1594 from NCAR/ejh_close 7ba458f3a fixed documentation 0cb6841dc turned on fortran netcdf integration tests 97d08bf6d Merge pull request #1593 from NCAR/ejh_ncint_async 10962543b protected use of nc4_file_change_ncid() with ifdef 0fccc80ab protected use of NC_UDF0 with ifdef 541d0df86 clean up 1d4cc195f got async working with netcdf integration with one computational component 63adee9ad merged changes from master 6c24f633f Merge pull request #1592 from NCAR/ejh_createfile_int_async ae9375900 now use PIOc_createfile_int() instead of PIOc_createfile() in pio_msg.c for async 9f91675e5 added contents of ncidp when ncidp_present to the parameters sent when a file is created in async mode ba2bb47db added ncidp_present to the parameters sent when a file is created in async mode d077e48fd added use_ext_ncid to the parameters sent when a file is created in async mode f5ee1625e fixed dispatch table removal of _pe functions b18bd1251 trying to get working 6e393976f commented out ncint tests ef98cca1d moving to async netcdf integration 86ad4463a Merge pull request #1588 from NCAR/ejh_fix_cmake 51217ec74 fixed cmake build from autotools build 8db71e74f added cmake directory to autotools build ed1d239d7 fixing Cmake builds a45f45f39 added config.h.in to Makefile.am cd0b55f2a Merge pull request #1587 from NCAR/ejh_fix fc4cdc347 last minute fixes 076231d37 Merge pull request #1586 from NCAR/ejh_version cf5a77724 changed versions for release 009fe0fe3 Merge pull request #1584 from jedwards4b/fix_integer_overflow 064e01acf fix an integer overflow issue reported on summit 7b2114eb8 Merge pull request #1581 from jedwards4b/netcdf_serial_bugfix a9245e838 must allocate on ioroot for serial io 04d8dc515 Merge pull request #1579 from NCAR/ejh_async_nc_create 4bea2db6d starting to get async working with netcdf integration 20457f902 Merge pull request #1578 from jedwards4b/fixtimerstop 2400bcce1 remove hardcoded timer name 24addf988 Merge pull request #1575 from NCAR/ejh_netcdf_includes e4a45016a now using only public netcdf headers for netcdf integration b4c74161d getting to work with latest netcdf-c 74e12ba18 adjusting to changes in netcdf-c with netcdf integration 8a91d30ae test cleanup 1a11dbf62 changed open/create to use ncid as final parameter instead of NC * b28779c66 removed include of internal netcdf file nc4dispatch.h cc5832b17 Merge pull request #1574 from NCAR/ejh_fortran_test_2 bbe69270e now getting darrays working from fortran with netcdf integration c64584ff0 fixed plain old PIO fortran program 6d92938d3 cleanup 7dd23b6eb added C test to guide fortran test building f067353ea Merge pull request #1573 from NCAR/ejh_example 1ef2e3781 Merge branch 'master' into ejh_example 49399c412 fixed example Makefile.am for C only builds 9ecf617b2 fixed example Makefile.am for C only builds 69226098f fixed example Makefile.am for C only builds f625222a3 got fortran example working 5404452f3 Merge pull request #1571 from NCAR/ejh_fncint_more_2 9f975e93b working on vard 21bced8fa getting darray write working 47a4e5e8c starting to add first vard 3279fd057 test development a8d20406e further test development 041316ba4 further improvement of test - now adding dims and var 8619790ba better error handling b20cbf24c better error handling 55424080f moving to use of iosysid 85ab319ef moving to use of iosysid c0dd8f4b6 Merge pull request #1570 from NCAR/ejh_fncint_decomp 934e19343 now use decompid in nf_def_decomp fcf2f7dab working version of nf_def_decomp fc4d65ec0 Merge pull request #1569 from NCAR/ejh_ncint_decomp 739c49e68 cleanup and documentation f47f9b170 working on nf_free_decomp bc125f81c more docs f004b234e more work on ncint, with inq_format functions f29d6b5da Merge pull request #1567 from NCAR/ejh_ncint_mem 0d892ef98 more documentation for netcdf integration b6591ec06 beginning to add docs for netcdf integration 740892799 changed nc_init_decomp to nc_def_decomp 233a8c968 changed nc_init_intracom to nc_def_iosystem fb21d5d0a changed name from nf_init_intracom to nf_def_iosystem 463740ab8 better memory checking for C ncint 91c056432 Merge pull request #1566 from NCAR/ejh_ncint_fortran_decomp b657f85cd fixed memory leak in ncint layer 2cfad5ea6 calling PIO_InitDecomp and PIO_freedecomp 65df82b23 working on initdecomp in fortran 95669126f Merge pull request #1565 from NCAR/ejh_fncint_more f1a3fe752 made nf_init_intracomm() into a function 91754ab3a made nf_feee_iosystem into function c8e538131 Merge pull request #1564 from NCAR/ejh_ncint_get_iosystem c14f8b7a1 getting nf_free_iosystem working better ec594c35e better handling of nf_free_iosystem 94d4b8756 Merge pull request #1563 from NCAR/ejh_ncint_next f71c1e9e0 adding nc_get_iosystem() cc3d53151 working on nf_free_iosystem 804aac23e adding nf_free_iosystem 227a81c58 Merge pull request #1562 from NCAR/ejh_ncint_fortran_next 1683f0d62 moving fortran ncint functions to their own mod file b35c6bbec moving fortran ncint functions to their own mod file f9a064ed3 Merge pull request #1559 from NCAR/ejh_ncint_fortran 70a219c9c Merge branch 'master' into ejh_ncint_fortran 213084b40 Merge pull request #1561 from NCAR/ejh_ncint_fortran_3 b4882a338 commenting out 31e6c8c72 trying cmake change 769257139 trying cmake change 973168279 trying cmake change f66530f83 trying cmake change ba8340494 trying cmake change 5b7769233 trying cmake change e3ca52b70 trying cmake change e45c9e4bb trying cmake change 6eed43177 trying cmake change 576be21fc trying cmake change 3ae508cc5 trying cmake change d212fe64b Merge branch 'master' into ejh_ncint_fortran b1ffbf19e Merge pull request #1560 from NCAR/ejh_ncint_fortran_2 d2add2efb better handling of netcdf integration in C lirbary 2469a2b30 better handling of netcdf integration in C lirbary e3d1a21a4 better handling of netcdf integration in C lirbary e6991ab2a trying to fix cmake build 1fffdf8de trying to fix cmake build 22e36e0d5 trying to fix cmake build f7cc7a424 trying to fix cmake build a9832f836 turning off netcdf integration in Fortran if NETCDF_INTEGRATION is not set by configure.ac a48cd4afd turning off netcdf integration in Fortran if NETCDF_INTEGRATION is not set by configure.ac 946c2fccc getting netcdf integration working in fortran e12d55a58 cleanup 392fb392a cleanup 3b08eb8fc finally got fortran working with netcdf integration! c08f6918b now linking fncint test to netcdf fortran library b0649bac2 further test development 259622303 developing fortran test of ncint e03d43f86 adding run_tests.sh script in fncint test directory 116f7de06 starting to test ncint in fortran ed9f6c538 adding directories and Makefile.am changes to support fortran netcdf integration 08e7b2b62 Merge pull request #1558 from NCAR/ejh_netcdf_3 acb666d76 more PIO_NCINT functions f5cc645f4 more PIO_NCINT functions 42f58b2b3 more PIO_NCINT functions e0051779e more PIO_NCINT functions c98429943 more PIO_NCINT functions c68712d20 more functions for netcdf integration layer ae6644623 Merge pull request #1557 from NCAR/ejh_netcdf_2 5c43ff5ca adding more functions to netcdf integration layer d8ff280ad adding more functions to netcdf integration layer 647baa20a adding more functions to netcdf integration layer 61cc130ad adding more functions to netcdf integration layer 267b96b02 adding more functions to netcdf integration layer 4b8dcd46e changed function names from NC_NCINT to PIO_NCINT bc3de414f moving functions around 8cd22e5ba move UDF initialization 974ed669b moved init of UDF to nc_init_intercomm() 4d3e937d5 made ncint test case 3D, now also reading and checking results 9852c2a3a Merge pull request #1556 from NCAR/ejh_pio_netcdf 6c704c58f added ncint_vard.c 7610f3875 merged master eaccc5557 now writing darrays with netcdf intergration 153ba17c2 Merge pull request #1552 from NCAR/ejh_uthash_include ff6a067c3 added nc_free_decomp 746f327d3 added nc_init_decomp 1205baae1 made test use 2D var 45ccb6179 added def_dim 92dd174ae got create working with netcdf integration layer ff53bf588 working on nc_create and the netcdf integration layer 2570fb4f6 adding create to netcdf integration layer 20bd34f8f now builds with logging f8c97103c merged master 1b08a2b32 Merge branch 'master' into ejh_uthash_include a29a28cb4 Merge pull request #1554 from NCAR/ejh_rename_log ffd5b57ae Merge branch 'master' into ejh_uthash_include ad2c869a0 fixed stray character ad9409f80 changed LOG to PLOG 8140b5b07 changed BAIL to PBAIL dbec51973 now close the file with PIOc_closefile() 886fee6a8 is it working? a3f925b27 adding argument to openfile_retry to tell it not to set ncid for netcdf integration layer files d72e8fb2a further test development d9014ad69 further test development 100af62ee further progress on netcdf integration 168edc66c now setting macro HDF5_PARALLEL for ncint builds to please ncdispatch.h 218f8e27e now running tst_pio_udf with mpiexec on 4 processors 0734badc5 more work on netcdf integration layer 36e51e748 further development of netcdf integration layer 2ad312e93 further progress on netcdf integration layer 50a24e2af more netcdf integration test development 17912911a now running tst_pio_udf.c bfc2062b3 added tst_pio_udf.c fb66aa3a4 working on netcdf integration layer! df9d5edd4 starting to add netcdf integration 07d2784e2 Merge pull request #1549 from NCAR/ejh_clean 904b56aee now install uthash.h f43cf8006 fixed warning b3e94d791 commented out some dead code f3bd166b6 Merge pull request #1548 from NCAR/ejh_travis_4 c64639931 turning on -Werror in FCFLAGS b8b52b9f5 Merge pull request #1547 from NCAR/ejh_travis_3 a0b4d5437 fixed example 2ad4aae70 turning on -Werror for C compiler 1994cde95 Merge pull request #1545 from NCAR/ejh_travis_2 9026e79c3 Merge branch 'master' into ejh_travis_2 dfae3652a Merge pull request #1544 from NCAR/ejh_travis_c_warning_check b8721df13 Merge branch 'master' into ejh_travis_c_warning_check 909be5d49 Merge pull request #1543 from NCAR/ejh_more_warn 8d1a6bdae travis is a pain! 29da02486 changed name of C library to libpioc.la ed19304da trying a warning checking build in travis f9fa38bc9 removed some dead code 82d900ae0 fixed warnings in piodarray.F90.in ddb92ef73 fixed warnings in pio_decomp_frame_tests.F90.in 4f0c73b7b fixed warning in driver.F90 80c569d69 Merge pull request #1541 from NCAR/ejh_warn_more_4 9ab5f539d Merge pull request #1540 from NCAR/ejh_warn_more_3 db8b2910b Merge pull request #1539 from NCAR/ejh_warn_more_2 062364722 fixed travis warning check f7641a948 fixed travis warning check d6b6a74b7 fixed warnings in pio_support.F90, turned on -Werror for C compiler in travis 78c88d243 fixed warnings in pio_nf.F90 b1dc7b252 fixed warnings in pio_tutil.F90 baf3bcb52 fix documentation problem 803c58584 fixed warnings in piolib_mod.F90 7ba85bd5e fixing more of piolib_mod.F90 warnings 14e2a55c1 Merge pull request #1536 from NCAR/ejh_err 4b766beb4 Merge branch 'master' into ejh_err ab6c5fe67 Merge pull request #1535 from NCAR/ejh_warn_6 56d915249 Merge pull request #1533 from NCAR/ejh_warn_5 b059b6d2d now find_region() returns error code, and takes pointer to regionlen as a parameter 3f3d5cb55 fixed a warning in pio_support.F90 776e5427c fixed warnings in pionfput_mod.F90.in 8df467ef7 fixed warnings in ncdf_inq.F90.in 04af202a0 fixed warnings in ncdf_get_put.F90.in 4fddb0b1a fixed warnings in pio_rearr.F90.in, some warnings from pio_decomp_frame_tests.F90.in 001640d3e Merge pull request #1529 from NCAR/ejh_warn_4 d5aa62448 Merge branch 'master' into ejh_warn_4 9a6b5ebf7 Merge pull request #1525 from NCAR/ejh_warn_3 5f4769b2f Merge branch 'master' into ejh_warn_3 2928ce362 Merge pull request #1517 from NCAR/ejh_warn2 8f3fe0035 fixed warnings in pio_rearr_opts.F90.in 3c6cea083 fixed warnings in pio_rearr_opts2.F90.in 6a6e814d2 fixed some more warnings in pio_decomp_frame_tests.F90.in 4e081851a fixed warnings in pio_decomp_tests.F90.in 3b1b0b0e1 fixed warnings in pio_decomp_tests_1d.F90.in 353762490 fixed warnings in pio_decomp_tests_2d.F90.in 32aaa7beb fixed warnings in pio_decomp_tests_3d.F90.in ad0c1935e fixed some warnings in pio_decomp_frame_tests.F90.in 85c7a4c7f fixed warnings in pio_decomp_fillval.F90 860807cae fixed warnings in pio_iosystem_tests2.F90.in b1eec4548 fixed warnings in pio_iosystem_tests3.F90.in 45bed2c60 fixed warnings in darray_no_async.c 32a1f4838 fixing warnings in pionfatt_mod.F90.in d648c55c9 changes that should not work 12d73c2a3 fixed warning in pionfatt_mod.F90 fa12cc250 fixed warnings in basic_tests.F90 e00730834 fixing warnings in piolib_mod.F90 c287ae7f8 fixed warnings in ncdf_tests.F90 393c5da0a Merge pull request #1502 from NCAR/ejh_bail d95813a35 using new EXIT macro for error handling 1886bc818 comment and whitespace cleanup cb2342865 moving more error handling macros to pio_error.h 7fbdb02c0 moving more error handling macros to pio_error.h 2695b4bc5 move error macros to pio_error.h bdfbb4139 removed MPI_Finalize() call from BAIL and MPIBAIL macros 43f7269bb Merge pull request #1498 from NCAR/ejh_mpe_4 78b0a4daf finished getting mpe working with test_async_perf c4cb0a110 adding more mpe logging to test_async_perf 57f23f2a8 adding more mpe logging to test_async_perf 5b46dab13 adding more mpe logging to test_async_perf 27044594b adding more mpe logging to test_async_perf a01cea380 more progress adding mpe logging to test_async_perf d751fe76f moved test mpe logging code to test_common.c fcef805cd Merge pull request #1497 from NCAR/ejh_mpe_3 2a0c8fcad more mpe logging work in test_perf2 2459f3a40 ifdef protecting mep log functions in pio_internal.h to prefent doxygen warning dba0dbaac doc fixes 398706873 more mpe work 06b41726c fixed mpe logging problem c8346412a more MPE changes cebb73d80 fixing mpe build e7ca36202 fixing LD problem 05eef3e92 mpe logging works ad4fd9af7 more mpe logging e8efdb453 more mpe logging bcbfecce3 more mpe logging 6c20479ec more MPE logging 3d9a11328 more MPE logging 4ce0b71f0 more instrumenting with MPE 0e0643b15 now logging init_async with MPE 1747d7fc7 running mpe with tests when available 3c32fbb60 starting to bring MPE logging into PIO library 6f0afaa48 Merge pull request #1496 from NCAR/ejh_next_version 67253c072 changed versions 7f1ae08bd changed versions bc7091a9b changed versions 539b7ea19 Merge pull request #1495 from NCAR/ejh_release b323420b7 merged changes from master 12bee91bb Merge pull request #1493 from NCAR/ejh_docs_fix 7942185b2 changed version numbers 7f16cf057 fixed fortran decomp docs ae8b17477 Merge pull request #1491 from NCAR/ejh_logging 337d32ade fix error handling b6522c40d now pio_init_logging() checks are returns error codes c2d842606 now pio_init_logging() checks are returns error codes a2897a08e now pio_init_logging() checks are returns error codes 2af631f15 Merge pull request #1489 from NCAR/ejh_mpe 992403837 whitespace cleanup bab1c8073 added MPE to test_perf2.c 513190a37 Merge pull request #1486 from NCAR/ejh_isolate_gptl 0cc7164ae no longer delete docs directory a8412c256 isolating GPTL calls 4f814ad7a Merge pull request #1481 from NCAR/ejh_cleanup_2 e0b1d8a29 fixing CDF5 issue 7b54b3eb3 cleanup of comments in pio_types.F90 03a258004 more cleanup for pio_types.F90 826de4599 more cleanup for pio_types.F90 e4cada78d starting to clean up pio_types.F90 0bf659948 Merge pull request #1479 from NCAR/ejh_cleanup 31a3ca060 whitespace cleanup de7396536 fixed problem attempting to remove docs directory 96bc111f5 Merge pull request #1476 from NCAR/ejh_even_more_docs_2 e5190c875 Merge branch 'master' into ejh_even_more_docs_2 cf2c4a741 Merge pull request #1475 from NCAR/ejh_even_more_docs 6a239a4a7 Merge branch 'master' into ejh_even_more_docs f75494945 Merge pull request #1472 from jedwards4b/jedwards/strnlen_fix c77ceac09 Merge branch 'master' into jedwards/strnlen_fix c37033647 removed unneeded prototype for removed function 4b7a1faa6 putting vard functions in appropriate place in docs df1218be4 separated put functions into category by var/vara/var1/vars/vard for documentation 030e7d455 response to review 6de0e9495 separated get functions into category by var/vara/var1/vars…

76c40a785 Merge pull request #1975 from jedwards4b/remove_protex a17a15327 remove unused protex markups f52ade075 Merge pull request #1974 from jedwards4b/fix_scalar_write_issue 3661a58bd derecho test script update 155be2fc9 update version 8b04e206f fix test for netcdf4 40bb45168 more github 1026fbd97 github tests again f01d36812 github tests again ab6c84b29 github tests again f1abc92cd github tests again d616e352a github tests again 3e6a435ad github tests again 20f1bcf94 github tests again 803298715 github tests again 24a9e1338 work on github tests e8d1be883 add derecho_testsuite.py 0ddbc2b8c fix scalar write issue, fix serial build issue 6d52a8c7d Merge pull request #1973 from jedwards4b/update/2.6.1 d9b6920e4 Merge branch 'main' into update/2.6.1 96a7d73d1 Merge pull request #1968 from jedwards4b/add_rpath 3d3a2f5dd Merge branch 'add_rpath' of github.com:jedwards4b/ParallelIO into add_rpath 3a4bfe06a resolve merge conflict ec1aef2c1 Merge branch 'main' into add_rpath 93b464bce update version 05e428451 Merge pull request #1972 from jedwards4b/bugfix/lustre 71b1fd248 try workflow again f377cab5c more workflow 10d4c3c67 fix for intel workflow 5b4717826 fix for intel workflow a42946660 add this back with a twist aa504dc8d add tmate for debugging workflows 513dbc8d0 fix ifort 1b68ba751 more cleanup 0bafcb4aa remove unused variables b4cb1ac34 update versions for github testing 3cf6ef570 clean up warnings 103a90991 more fixes for netcdf serial c45c4406a some fixes for netcdf serial bld 2cbf4bd0d potential fix for issue in branch bugtest/lustre 25b471d58 code changes to demo lustre performance bug ff7a19f21 add rpath variables to cmake build f45ba898b Merge pull request #1963 from jedwards4b/pio2.6.0rc1 a644bb61e update version d858d79d5 Merge pull request #1953 from jedwards4b/netcdf_integration_v5 4ac2b0e07 confusion about spack version 4fe8d187e confusion about spack version 020bfa712 skip test timeout pio_rearr_opts 2bd2c5d00 @develop should be @=develop (new change in spack)" ac3b0595b fix spack? 5e7a91e26 fix action b5244a576 spelling error 52e31e60a smarter about building parallelio 4003a79ea try this e0befe62b add tmate to debug eaffcf10f fix have_par_filters e437a94e7 fix some tests 95d9cf5c4 try this bc9534cb3 still trying bb08a8ff9 Merge branch 'main' into netcdf_integration_v5 cd8d7dbe9 remove unused arg 11c179e38 change test for par filters 11fc9d0a3 fix ifdef in fortran 38b8fef66 remove unused variable f240e34ef wrap filter_info 53462645c more cleanup 7390ec03d update autotools 77b579907 more cleanup f49d8ffbc reduce compiler warnings 3732b7c2b add test 3a0b1cd94 commit to move to gust 744bf5c3e Merge pull request #1962 from NCAR/jedwards4b-patch-1 c11ae47e9 Update README.md 44ab3d79b add pre-commit hook 30c3018a7 reorder to fix syntax error cdb55c733 prepare for pio 2.6.0 a5cbb28a6 add these and go to hackathon branch ad613dc55 add szip a16ca795f WIP 6af9cc985 cmake builds again 86101f2de add test for nc_inq_filter_avail 7119ddac7 more macro fixes 2247b3e65 more macro fixes fc8015f95 fix macros aede8723c fix testing again c0b49af55 add filter and quantize to fortran interface 02268a9fc add filter and quantize functionality 21cb6675d fix intel netcdf-c build f48a38b93 add back netcdf build 8c95ae17a try this 19e071bbe work on testing workflow 40ae6f019 update actions 152a0cf62 update actions cfc271e7c update actions 3b47163a6 update actions 6f88afa3b make it backward compatible 18eca188e fix the test 83176df55 add test, expected to fail 11a68cbd5 more fixes 6cf3810fe more fixes bd4517351 skip this test 6bb3a9b02 skip the check 93d82ad5e try again 3ffdd8124 more debugging 68b9a646b more debugging ab4ee59f5 try this 977ef90bf more fortran fixes dae38cdef more fortran fixes 3030489ea more fortran fixes cf92770d1 more fortran fixes dbc46c3f2 more fortran fixes ff513fbef fix fortran warnings 99fb47ac2 make it backward compatible abe19445a fix fortran warnings 6c8aad764 fix fortran warnings 54c3b8fab fix fortran warnings d0b8e5ebe fix fortran warnings 03079e75f fix fortran warnings 060fee736 make it backward compatible 09c5ded0a resolve merge conflicts d69dbe0ac passing all tests with NC_DISPATCH_VERSION=5 753464d2e fix declarations 77055f9e1 commit to try on cheyenne 7bce0e534 only run ncint tests for netcdf4 in netcdf4.9.0 and older 1747a4758 adding new filter functions 52649df69 determined test failure due to mpt/2.25 bug 781978d99 support versions 2-5 620f6741b Merge branch 'netcdf_integration_v5' of github.com:jedwards4b/ParallelIO into netcdf_integration_v5 3fd1b3e4e fix parens c404de8dd Merge branch 'main' into netcdf_integration_v5 2275ad951 stuck in testing 05173a655 Merge pull request #1952 from jedwards4b/master_to_main d3f134936 replace master with main 2446bf96c Merge pull request #1951 from jedwards4b/external_actions_squash 4fc7cd3d4 with -> enable e3e3ca7b8 fix type in workflow 4bdd79ca8 fix cache 1288017de squash commit of external_actions fd1bdf842 Merge pull request #1949 from jedwards4b/pio2.5.10-candidate 21a0f7015 update version patch to 10 126beaeee Merge pull request #1944 from billsacks/fix_default_mode 64666d199 Merge branch 'master' into fix_default_mode 6fcb613a2 Merge pull request #1946 from jedwards4b/update_github_tests c73a4d63c remove redundant test 490565b4f once more 2f95d78aa fix ldflags d1138cb57 try ldflags 79df169fe try fflags instead 20a223277 add -static-libasan 830f226bf remove memory violating comment b7745d637 update address sanitizer runs 74203a41b oops wrong hdf5 version 53c6eec31 more github action tuning acc462641 more github mods 87e0e9432 netcdf integration currently only works with netcdf-c 4.7.4 6f5d6b340 need both FFLAGS and FCFLAGS? 647e68cdd try this 9a9db159b try this 877f691c7 try this 5a4d06c11 more github action fixes 0eac1ebb9 try run-name here 8abc70dc7 fix yaml formatting issues a2a7a1132 change FCFLAGS to FFLAGS ce5faf9cb try removing name and adding run_name 0e91b5e4d remove name use run_name dee848ba1 update checkout and cache actions 9a63af64f update run-name 2fafb1581 update software versions 95553d71f update github tests to use -fallow-argument-mismatch bbfe1b221 Fix default value of mode for PIO_openfile df1c069fa Merge pull request #1941 from ACCESS-NRI/pkg-config 48baa2b29 backup search of NetCDF using PkgConfig 157e559ff Merge pull request #1937 from jedwards4b/cmake_version_revert eef316fb2 make work with cmake 3.5.2 (esmf requirement) a61c76304 Merge pull request #1936 from jedwards4b/version_update a342a931d update version tags 6ab657ab5 Merge pull request #1935 from jedwards4b/update/spack_experiences df5ced6e8 shared lib as default leads to problems linking gptl 586fd2509 add CMAKE_POSITION_INDEPENDENT_CODE 9fd941936 Merge branch 'master' into update/spack_experiences f43b5a8d8 Merge pull request #1928 from kgerheiser/patch-1 e96aa094a change malloc to calloc for tmparray 66478b875 updates based on experiences with spack package f18736b64 Merge branch 'master' into patch-1 07d5d1658 Merge pull request #1932 from jedwards4b/updateto258 0767c56bf Merge branch 'master' into updateto258 741f01b06 Merge pull request #1929 from jedwards4b/readonly_init_decomp 42463401c update pio version to 2.5.8 fe8526389 turn off doxygen build in test 2e9e8d659 Merge branch 'readonly_init_decomp' of github.com:jedwards4b/ParallelIO into readonly_init_decomp 3e832ff92 turn off doxygen warnings 02fa28809 remove halo in test b033009c9 remove halo in test 8315a9583 revert netcdf version 992d5970d add debug flags 793c83be6 try again d292334f9 try again 98b30a053 looking for mem leak 5bd5cfb0e initialize exp_val 295b5da30 testing memleak issue a25ef8105 more doxygen 4f206ecac update docs a9dc65d65 try this 1dd48891d cleanup fortran interface 216faa114 fix format bf342d0bb Merge branch 'master' into readonly_init_decomp 72d31a229 add new file to autoconf build da18105e6 add the pioc_async.c file 11df9a2ff Merge branch 'readonly_init_decomp' of github.com:jedwards4b/ParallelIO into readonly_init_decomp adb084450 add a test for initdecomp_readonly 0eb7ad638 copy back from ESMF develop cd9dae11a Add BUILD_SHARED_LIBS option c3c042e32 Merge pull request #1926 from climbfuji/feature/update_license_to_apache2 23153d5ba Replace COPYRIGHT file with LICENSE file in Makefile.am db104184d Remove old COPYRIGHT file f09ce7d09 Create LICENSE c5d622612 Merge remote-tracking branch 'mydev/startlist_err_fix' into readonly_init_decomp 9215ad2f7 remove debug print statement 10c08240e better fix de3bc6ff5 debugging workflow eeaa57f4b debugging workflow 6ce4184cf debugging workflow 5de7f424c debugging workflow f97ef84d1 fix an error in computing startlist and countlist for pnetcdf e3d835e1e an attempt to reduce memory consumption and improve performance d13e39116 Merge pull request #1924 from jedwards4b/move_to_heap 233c141bd move this allocation to the heap 6954d2f6f Merge pull request #1923 from jedwards4b/version_257 8986c3174 update version to 2.5.7 ec0878108 Merge pull request #1922 from jedwards4b/change_cmake_minimum 959dcfc6a closer to requred cmake minimum a91d94c12 Merge pull request #1921 from jedwards4b/parallel_sort 8e1220f16 undo debug change a95b5b602 fix conflicting types c0e367b20 fix conflicting types ff14c8f26 cleanup and debug 6cb1b45ca remove check for size of MPI_Offset 5bc2d18bd debug github workflow 92ad82b5a debug github workflow aae9abfd0 remove debug print 41ee148f1 cleanup cd2e3ff37 add a comment 6f36ec155 fix run_unique_check dedf05a53 only check readonly on compute tasks 8ea3ec589 add parallel_sort to autoconf build 83f1d1482 Merge branch 'master' into parallel_sort ef4bebd9d consider this change, not yet working 5cd4f369a Merge pull request #1920 from jedwards4b/update_cmake_minimum f12a7c603 fix compmaster test 2ae945860 fix compmaster test 7edc061ba fix communicator 38f85db2d need to check readonly for subset c913401f8 only add fortran dependencie if fortran build enabled 9141ce508 clean up testing 628a60805 update minimum cmake version, based on the oldest I can access a95907685 Merge pull request #1916 from jedwards4b/remove_MPI_Offset_redef f6faded05 remove the redefinition of MPI_Offset and MPI_OFFSET 0dbdf3b43 Merge pull request #1915 from jedwards4b/update_version_2.5.6 949c4acde update version to 2.5.6 f49656d57 Merge pull request #1911 from jedwards4b/subset_rearr_fix fbd8a0a54 a little cleanup 2f106a310 fix in esmf mesh read 907954dea improvement 36d85f710 fix for subset rearranger bug in 2.5.5 fa73d277e Merge pull request #1906 from jedwards4b/fix_netcdf_src_path_for_workflow e136d362c fix it again ebc8c9009 revert configure, test github caches - all workflows passing 2ca91d809 add hdf5 version and dependancy 98bb52f88 more github action fb8172f29 fix cache 1f242695b fix libpath maybe 8cf23ae93 backout 4.8.1 use 4.7.4 ada3d061b more netcdf download 87a2a1105 get netcdf from github not unidata site a755d3a38 get netcdf from github not unidata site ffaeefe93 update NC_DISPATCH_VERSION c75831cea fix line return issue 63e54ed05 all netcdf downloads now updated 255657ced add oversubscribe 3bb48a798 cut and paste b67943796 cut and paste 758e18665 reformat with yamllint d0978d431 reformat with yamllint 924b80d3f reformat with yamllint 4f1fe5f62 reformat with yamllint 936bc928f reformat with yamllint e6837b890 reformat with yamllint 1c2236b8f reformat with yamllint a03b0bfba try again a9ad7893b try again 9a26ba14a try again 4a65c35c6 update netcdf download path e352fd214 Merge pull request #1902 from jedwards4b/64bitdata 5e6aa9037 #define PIO_64BIT_DATA NC_64BIT_DATA requires netcdf 4.4.0 or newer f50f03872 Merge pull request #1899 from jedwards4b/add_write_nc_decomp_support_fortran 776de3e5c move these to a seperate repo b70ffd283 add the decomps using lfs 9737b204d add decomp files using git lfs d3a8ec8da Merge branch 'master' into add_write_nc_decomp_support_fortran bb253aba2 add pio_finalize call a4ed64c14 Merge pull request #1896 from jedwards4b/pio_buffer_size_limit_rename d8da2d2b3 Merge branch 'master' into pio_buffer_size_limit_rename 97ea899d7 Merge pull request #1897 from jedwards4b/fortran_deletefile_returncode 9576b8533 fix documentation 79b24b3c7 make fortran_order logical 469cfcba6 add fortran interface to nc dof read and write routines, add a translate program 8b45af91d begin add fortran support for this 58c45f968 document new parameter 10b733273 fortran pio_deletefile return code, optional for backward compatiblity 51524e5d7 rename pio_buffer_size_limit to pio_pnetcdf_buffer_size_limit c1307bf21 Merge pull request #1887 from NCAR/ejh_version 1175c39c9 Merge branch 'master' into ejh_version 0fb64ab47 Merge pull request #1891 from jedwards4b/refactor_subset_method 765557a91 Merge branch 'master' into refactor_subset_method 856fb305e remove cperf from tests 226dbe93f debug cleanup badc1c033 changes for serial build dbb3e5440 document new routines acc35223b document new variable da1cb8ce5 Merge pull request #1886 from jedwards4b/address_sanitize_patch ad2819e59 undo whitespace changes 1e50df7e0 undo whitespace changes d304db9b7 undo whitespace changes f249286e4 undo whitespace changes f95d648b4 cleaning up b48c44e62 Merge branch 'master' into address_sanitize_patch e99ffcb1c working for SUBSET rearranger b8bfef8e9 continued development of piodecomptest 0f3214a35 an attempt to refactor the subset rearrange method a1526a296 Merge branch 'master' into ejh_version 877986194 Merge pull request #1883 from jedwards4b/pio_byte_to_mpi_signed_char c6d90dd8f changed version to 2.5.5 870649ba5 fix bug in pioc_read_nc_decomp_int 0e3762da5 remove tabs from file 1e21296cc fix an issue exposed by address sanitiser 699c65187 remove travis test documentation 35a5339a8 remove travis test ecf94f315 update tests adding pnetcdf for BYTE and CHAR 982e77468 pio_byte type should be mpi_signed_char and not mpi_byte 468c06a59 Merge pull request #1881 from jedwards4b/cmake_fortran_cleanup 6d518a071 Merge branch 'master' into cmake_fortran_cleanup e4087a375 only do cmake fortran if building fortran interface 6ffa5d1b1 Merge pull request #1879 from jedwards4b/cray_compiler_fix 297c5d096 fix inconsistancy in intent 4dafb796e Merge pull request #1876 from NCAR/ejh_ranlib 4586f2cf8 fixed overflow in test e85dc3785 Merge pull request #1875 from NCAR/ejh_fix_dist 2c67ab15a add exampleAsyncPio.F90 to the autotools build fc1a67924 Merge pull request #1871 from kgerheiser/bugfix/macos-common-symbols 7e2e00a6c Merge branch 'master' into bugfix/macos-common-symbols 77a1ea044 Pass -c to ranlib to include common symbols on macOS 6d4bb2879 Merge pull request #1870 from NCAR/ejh_fix_dox_version b05b483c1 fixed version 0dc7d8ff8 Merge pull request #1869 from NCAR/ejh_release a2bd6367a updating versions 357ca506c Merge pull request #1864 from jedwards4b/check_netcdf_errfix 9a4e836ca try this 59ad3368c cmake still failing add debug code 0638adedf set WITH_MPIEXEC --oversubscribe 35c04b6fa set WITH_MPIEXEC --oversubscribe a06dfa2de add oversubscribe option 73716f7e4 try --oversubscribe d44762937 revert change to strict autotools workflow c9a944862 Merge branch 'check_netcdf_errfix' of github.com:jedwards4b/ParallelIO into check_netcdf_errfix 4fe2cd24f merge master for workflow fixes 550160bca Merge branch 'master' into check_netcdf_errfix 813e7c159 Merge pull request #1860 from NCAR/ejh_2 264242b58 refreshing caches d86865dee refreshing caches faebeea33 refreshing caches 6ea34b9e4 refreshing caches 03ff8f545 remove enabled-shared pnetcdf option 8d44884f3 try fix for pnetcdf fac7ee7dd fix error in check_netcdf call and in detecting dap 612014640 Merge branch 'master' into ejh_2 0ec340c76 Merge pull request #1859 from NCAR/ejh_versions c67d8c279 resetting caches 1b901c0db triggering CI 2bab8b463 one more try 7accbbad3 updated version numbers for release of 2.5.3 53497cafb Merge pull request #1857 from jedwards4b/pnetcdf_support_cmake 6f0b9bf16 fix indicator for pnetcdf support in cmake c77a30d95 Merge pull request #1855 from jedwards4b/create_logfile_only_if_loglevel 983bd8e66 only create log files if log level > 0 989e026f5 Merge pull request #1854 from jedwards4b/redef_from_def_test 7df2e2afe remove this test, no longer valid 360a360ac Merge pull request #1852 from NCAR/ejh_readme af9b0733a commented out test_async_1d ca842d15a commented out test_async_1d 66132141f updating readme 5206ff4c5 updating readme c6fd1755c updating readme 47f466fd1 updating readme 8b2f798a4 Merge pull request #1851 from NCAR/ejh_cmake 4ea3f9362 turning on netcdf integration in cmake build 304b7296e Merge pull request #1850 from NCAR/ejh_next_1 2123df499 turned test code back on 40d9637c2 Merge pull request #1849 from NCAR/ejh_next 582d6f7b6 turned test code back off 0a41fbf89 turned test code back off d7eb8207b turned test code back on 41ac8bc7f turned test code back on 2f90688c7 turned test code back on 9f6b1b5c9 fixed type size in async code 16b469d00 turning test code back on 268c69929 Merge pull request #1848 from NCAR/ejh_preprocessor 558f24000 cleanup of automake and pre-processor symbols e8a87005b removed pre-processor symbol USE_NETCDF4 77a31b1bc Merge pull request #1844 from NCAR/ejh_no_pnetcdf_build 818eead20 commented out part of tst_async_multi 7b0b78b16 commented out part of tst_async_multi 41ea01e99 commented out part of tst_pio_async 388681f92 commented out part of test_async_1d 34f6b99db fixed no-pnetcdf workflow, renamed ubuntu latest workflow 463e37d4e adding new workflow dddf14773 Merge pull request #1843 from NCAR/ejh_warn c95152b6e fixed warnings and netcdf-integration build without pnetcdf 2d0c61c2e Merge pull request #1840 from NCAR/ejh_cmake_again_3 444c30dc4 fixing cmake workflow b43e67e44 fixing cmake workflow 42366fb63 Merge pull request #1836 from NCAR/ejh_cmake_again dcaba92f8 changed test timeout in cmake 19570c281 fixed code warning, removed print statements from test f632317cd make configure search for netcdf-fortran if --enable-fortran and --enable-netcdf-integration are used 57446873a debug test 9b5964267 add fortran build c6912419b fix paths 3705bbdf2 adding fortran f65e972e4 adding fortran d914a8353 adding cmake build 9accccb00 Merge pull request #1835 from NCAR/ejh_cmake_fortran_workflow 27d20a3be try a different cmake? ee9fe1b61 giving up on cmake build for now ebfb0e503 adding another cmake build 8fd204e80 adding another cmake build 219d72fb9 adding another cmake build ed0304884 turned off fortran in cmake build b56162ef1 fixed fortran test 5c34c279f turning on fortran build in cmake workflow ee329568b Merge pull request #1833 from NCAR/ejh_ncint_test_2 85f50f29d more testing da6015c2c Merge pull request #1831 from NCAR/ejh_ncint_test 11959c931 fixing ncint test for 4.7.4 by commenting out code 8dbde41a0 fixed comment ccbb2302f fix test_darray_multivar3.c 7172df901 turning on netcdf integration in workflow e53623410 Merge pull request #1826 from NCAR/ejh_test_more 1eb5a219d working on workflows 40ce8ea26 switching to pnetcdf-1.12.2 593e85371 adding testing 0f0558ffe adding testing 0f3502fa0 adding testing 862538461 Merge pull request #1823 from NCAR/ejh_more_tests 71a695cba working on asan build 70066f238 working on asan build b5801cd8b working on asan build 8fd651963 working on asan build a679c5bd5 adding testing with hdf5-1.10.7 3308d5e93 renamed workflow files to reduce confusion f34ef23a9 merged master 0887324d4 fixed warnings, trying to get asan workflow to build 6947e3114 Merge branch 'master' into ejh_more_tests d862880a7 added asan testing e341609e3 Merge pull request #1821 from NCAR/ejh_test_on 1464bf0a4 Merge branch 'master' into ejh_test_on ef34338ae fixed test_darray_multivar3.c 2d6de331b fixed test_darray_multivar3.c 1ef9493f0 Merge pull request #1820 from NCAR/ejh_default_blocksize 9e492a483 changed default blocksize 36eba03fa Merge pull request #1817 from NCAR/ejh_docs c7b3010cc documentation improvements 082fc0f32 documentation improvements cacb65e7b documentation improvements 9548daac5 fixed warnings in code 4200f55a1 Merge pull request #1809 from NCAR/ejh_perf_more ce23930d6 now setting chunksizes for netcdf4 performance runs f59373773 whitespace cleanup 6f7a1dcdf fixed mpe problem in test_simple.c 9a669de89 modification to perf program output 9abd0ca71 Merge pull request #1806 from NCAR/ejh_perf 329ef8f2d cleanup 9f912f859 merged master be3b13f22 fixes to test_perf2.c 84511247c Merge pull request #1805 from NCAR/ejh_fix_test 5df3c5dc6 whitespace cleanup 118e44a76 better async error handling in tests 57c03b9c3 whitespace cleanup 379983a92 more fixes for async test error handling 9bdf340a2 more work on async error handling 25d5bf4f0 more work on async error handling 3b550c794 more work on async error handling f83540176 more work on async error handling bb6adea7f fixed comment b44d3237c better handling for test failure in async tests 40da636a3 added AERR() macro for errors on async tests d8ec81a98 fixed comment 9cec790f1 fixed whitespace issues in pio_error.h d14471895 fix printing of some incorrect error codes in cunit tests 9dad4e97a Merge pull request #1802 from jedwards4b/avoid_msg_starving e6fc3e00b clean up test 90f497c14 change waitany to waitsome to avoid message starving 53bdadcbf Merge pull request #1800 from NCAR/ejh_docs_2 dd1b8d038 updated documentation and cleaned unneeded preprocessor symbols from test_perf2 and test_async_perf 5d0f8a5b0 Merge pull request #1799 from NCAR/ejh_t1 eec9e0b50 stop running test_async_perf with other CMakeList.txt tests c254d12f0 turned off logging in test e86c55cb6 try reducing the size of this test 358e71917 document new error code b51b8324c move large allocate from stack 4f01bc28b fix test 570abae1e add error for rearranger mismatch in async mode 564a15116 fix async_perf test 860f6f99f Merge branch 'more_async_tests' of github.com:jedwards4b/ParallelIO into more_async_tests a8493e337 add test_async_perf to cmake build 66564a550 Merge branch 'master' into more_async_tests 5852d9093 Merge pull request #1765 from t-brown/master 40da5e29c add SUBSET rearranger d741f3700 Merge branch 'master' into master 1a3fa8630 Merge pull request #1794 from NCAR/ejh_fix_perf 2184073b0 Merge branch 'master' into master 2a2a08dad turned off subset rearrarger in test_async_perf b51f6768c more improvements to performance programs 6a29e16eb merged master f0a9c0ad1 fixing test_async_perf 5ca0b5586 Merge pull request #1791 from jedwards4b/async_subset 6b08ffb66 now test both rearrangers in tst_perf2 d956b7904 added commas to output 7e385d133 fix test bbe58daf7 add tests c8f91fbca subset working in async 744b73163 Merge pull request #1790 from jedwards4b/add_nf_pio bbb9ed716 remove need for netcdf or pnetcdf fortran libs 53d652ed8 add netcdf fortran build 5d1ca6791 add nf_pio, netcdf now defines cdf5 format 8a0cb4f84 Merge pull request #1786 from jedwards4b/sort_only_on_compute 3d49f3008 array sort should only happen on compute tasks 7f28489f5 Merge pull request #1784 from jedwards4b/add_async_get_att_test 4b79b0203 add new function to include file 15921d6ff fix documentation biff d937cc331 add global_set_log_level, fix issue 5cd85396f add async test for get_att - test currently timesout 38d9acda5 Merge pull request #1782 from jedwards4b/async_fixes ffe4098c1 move malloc to correct location e05d8f2b0 remove unneeded change 7806081b4 changes for async interface 7e242f78b Merge pull request #1781 from jedwards4b/with_pnetcdf_cmake 6c4d85875 use WITH_PNETCDF in CMake build f960b3799 Merge branch 'master' into master 1d0dabdf3 Merge pull request #1778 from jedwards4b/add_pio_init_async_from_comms 1de5ded13 Merge branch 'add_pio_init_async_from_comms' of github.com:jedwards4b/ParallelIO into add_pio_init_async_from_comms 7a52d1d9d try this 875966b5b fix mem issue 60f9f17f3 fix documentation f63773317 remove .f90.in from gitignore file, add tests cf09cd22d remove unused var 7f28e28cf fix Makefile.am 8af4d74d9 try again 2d3cb219a fix test generation issue 4a012a898 add test to autoconf 155c11dee fix line length issue 01e9e31dd add async test from fortran bcc711331 remove set_log_level from test 8f10a32a2 remove debug print ea404f6b3 add PIOc_init_async_from_comms and test 53c5a2c23 Merge pull request #1776 from jedwards4b/update_f_examples 0f5da9dc3 Merge branch 'master' into update_f_examples a8acfd49d more doc cleanup cad018af7 more documentation and refinment 4fd48cfce add some documentation 9e999911c correct ranks in async 0f65ecc0d cleanup a27009b57 working example from fortran 81c778517 Merge pull request #1774 from jedwards4b/unique_name_err_buffer e079cb408 make example resultlen distinct names from that in pio_error.h c30ff49c5 make example err_buffers distinct names from that in pio_error.h e26c200c2 work on async interface 092a618ee begin work on fortran async interface 66449308c Merge branch 'master' into master 7309b9b60 Merge pull request #1772 from jedwards4b/more_fortran_interface c59a6d644 remove bad assumption 0a565e497 more fortran interface changes 2d4202846 remove debug print c9e5d01aa fix nfget 74afc2a9a cleanup c7813144d fix test var io from fortran 1caa8c15c add pio_fill 134c5209d Merge pull request #1771 from jedwards4b/fortran_interface_updates c91eb59c0 back out setting of fillvalue in pio_darray f3b63c9cc untabify 01830e4eb fix whitespace 5ae954910 try again 94ff81b6a undo last change and see if travisci will pass 91520c20c read_darray sets fillvalue 736c0745c add target attribute 7bd521922 more minor changes 0ba4b787d implement pio_inq_var_fill in fortran, add tests e7d621b0b Merge pull request #1769 from jedwards4b/cdash_test_fixes 3eac73356 undo unessasary change 3d8956df3 fix pgi version and openmpi test error fed328b7c Merge pull request #1767 from jedwards4b/update_cheyenne_tests e47b8f108 update cheyenne modules for ctest 364a445bf Adding an autoconf check for C99. c90a7a287 Merge pull request #1761 from jedwards4b/remove_pio_use_malloc 3e432479a untabify c files b7b9b52e1 untabify pio_darray.c 9fc01568a Merge branch 'master' into remove_pio_use_malloc b241756e7 Merge pull request #1763 from jedwards4b/fix_int_overflow 1c9dd2823 fix integer overflow issue noted in nag compiler 9d3470f5e fix doc generation error 34809b99a fully remove pio_use_malloc macro b9855cdb5 Merge pull request #1759 from jedwards4b/add_flib_set_fill 78d28a329 add set_fill to fortran interface 6f9fb5e Merge pull request #1754 from NCAR/ejh_release 9efeee4 changed version numbers and so library numbers fd8b8c1 Merge pull request #1753 from NCAR/ejh_no_compress 00104f8 no longer turn on deflate for vars automatically d0d4a98 Merge pull request #1752 from NCAR/ejh_bget d048ed5 working on cmake test build cbf9b17 working on cmake test build 4c54550 merged 14672d4 working on cmake test build a98bf4a Merge branch 'master' into ejh_bget 14ba346 Merge pull request #1751 from NCAR/ejh_docs 668bdd3 more bget fixes c992327 added cmake to test build bad9cee removed bget 2f3ed11 removed bget d23ae96 more fortran doc work d751d49 improving fortran docs e97f239 improving fortran docs 3a77973 Merge pull request #1747 from NCAR/ejh_ncint_deflate 73eaa0c added endianness f97e666 now testind def_var_endian 9c88c0e now properly getting chunksizes thru ncint c298e79 developing test 09dc756 added deflate to the test 5853389 modifying tst_var_compress f11724c added tst_var_compress.c 39b0940 merged master 64cdf4b Merge pull request #1746 from NCAR/ejh_mpi_check 286f529 removed cmake build from github testing c2492f1 dealing with der_var_endian and def_var_chunking in netcdf integration layer 245a212 adding PIO_NCINT_def_var_deflate b25c930 added check for MPI c569627 Merge pull request #1743 from NCAR/ejh_more_tests_2 261d8b6 increased time-out c6c6138 added cmake build to a4.yml adbb0d8 removed flags from fortran cmake build 63662f5 Merge pull request #1742 from NCAR/ejh_flags 666731d removed unused VARN pre-processor defines 3ce5db5 Merge pull request #1741 from NCAR/ejh_more_testing_2 81de16e adding Fortran to build summary 6ec562a MPIEXEC in examples/f03 directory, also set FC in fortran build e835926 turning on fortran build in github CI, also fixing mpiexec in tests/performance a5fb922 handle mpiexec for fncint and general dirs 9e4a39e trying to get gcc version 3c02032 Merge pull request #1738 from NCAR/ejh_more_testing eb23c9f fixing order of chunksizes 15a191b fixing order of chunksizes e37d19a fixed chunksizes type size error in F90 api 13cb7c7 fixed shell script with new test name f1e58bd renamed test 5ff9844 fixed docs 5c2ae65 adding pio_inq_var_chunking 6675467 more test development f114fbc further test development a54de42 further test development cbed988 further test development cdc01a1 turn of netcdf integration in github workflow 05ce8e3 added ftst_vars.F90 to CMake build 9d3ff03 added ftst_vars.F90 to CMake build e9f4f75 starting to add ftst_vars.F90 2987785 turning on ncint f6feb76 Merge pull request #1737 from NCAR/ejh_flags_next 5f8e9fa more testing in new workflow 71eace1 more testing in new workflow c2919cb more testing in new workflow 87e38c5 more testing in new workflow dd0400c more testing in new workflow 1733a7a adding mpich workflow a31c6f8 adding mpich workflow 138f4f1 adding mpich workflow d677d07 adding mpich workflow 28429a5 fixing MPIEXEC in library summary for CMake builds 22d1160 Merge pull request #1735 from NCAR/ejh_cmake f130a86 adding fields to build summary f835a8d removing unneeded logging pre-processor macro from CMake build 9d8c81a clean up 1b788c9 more fixing for flib and clib, now fixing _PNETCDF e6960d9 more fixing for flib and clib 1bb4b57 now fixing for flib 510e955 fixing CMake determination of _NETCDF4 843f6d9 commented out more unneeded flag setting in cmake adf6308 commented out more unneeded flag setting in cmake 6d767b2 commented out more unneeded flag setting in cmake d37b976 taking away flag from CMake build 54ee841 Merge pull request #1734 from NCAR/ejh_doc_fix 35742c6 now ncint tests repect WITH_MPIEXEC 151affd now ncint tests repect WITH_MPIEXEC 181373a fixing docs, cleanup of test workflow e715d07 Merge pull request #1733 from NCAR/ejh_openmpi_2 7b874db clean up 7ddbfe7 trying to deal with MPIEXEC in CMake 41b1588 trying to deal with MPIEXEC in CMake 280c4b9 trying to deal with MPIEXEC in CMake b501e62 trying to deal with MPIEXEC in CMake 7bcf9f3 trying to deal with MPIEXEC in CMake f5906b1 trying to deal with MPIEXEC in CMake 672259c trying to deal with MPIEXEC in CMake 4815763 trying to deal with MPIEXEC in CMake ba379cc trying to deal with MPIEXEC in CMake 2138bd3 trying to deal with MPIEXEC in CMake b2820c2 trying to deal with MPIEXEC in CMake e802925 trying to deal with MPIEXEC in CMake b1fabee trying to deal with MPIEXEC in CMake 4174cf9 trying to deal with MPIEXEC in CMake 7422324 trying to deal with MPIEXEC in CMake deed510 trying to deal with MPIEXEC in CMake d561d64 trying to deal with MPIEXEC in CMake c0466f9 more work on cmake build 6eb1b7a more cmake build 1ac66e0 more cmake build 51791cb more cmake build fc04c72 more cmake build afb423b more cmake build ddb380f more cmake build 9e654d8 more cmake build 4c1ca9e more cmake build feada9c more cmake build f2bbbbf more cmake build e23ce03 more cmake build 1013818 more cmake build 081b863 more cmake build 36b7c7b more cmake build f38d8ae more cmake build c16d88a more cmake build 7f547ee starting to add cmake build of C library 00e667f Merge pull request #1731 from NCAR/ejh_openmpi 0f2db9d converting more tests to use new --with-mpiexec option c7fc47a converting more tests to use new --with-mpiexec option dc8275d converting more tests to use new --with-mpiexec option 2af2aeb adding tests/cunit/run_tests.sh.in db613c3 adding tests/cunit/run_tests.sh.in e4fb33c adding --with-mpiexec option to configure 2d908a1 adding --with-mpiexec option to configure d76dd49 trying to get openmpi mpiexec working 3822956 trying to get openmpi mpiexec working 558a3b9 trying to get openmpi mpiexec working ba2b719 trying to get openmpi mpiexec working 493353a trying to get openmpi mpiexec working dcb5e08 trying to get openmpi mpiexec working a96671f trying to get openmpi mpiexec working f283a80 trying to get openmpi mpiexec working 0903e62 trying to get openmpi mpiexec working 5a96af8 trying to get openmpi mpiexec working 2d9bf6b adding PIO b35ee21 adding PIO 2bf634f adding PIO cc1dc81 adding PIO 8b243ca adding PIO 3681f56 adding PIO 0c5dbbd adding PIO 1120342 adding PIO 8984b26 adding PIO 7a5c3f3 adding PIO 8f86595 adding PIO 4d1a709 adding PIO 61ef8de adding netcdf-fortran and pnetcdf 6d2b2a9 adding netcdf-fortran and pnetcdf 35dda9d adding netcdf-fortran and pnetcdf 49ab2d7 adding netcdf-c 1199dd3 adding HDF5 1c5ab76 adding HDF5 ae45f2b adding HDF5 ab77827 adding HDF5 dc6eb09 adding HDF5 2b766e2 fixing apt-get for curl 5d9b54b building openmpi 0697d04 building openmpi 0043527 Merge pull request #1725 from NCAR/ejh_next_9 41b62fb fixed warning, turned of -Werror for fortran to try and get github workflow building c76f148 fixed warning, turned of -Werror for fortran to try and get github workflow building 32640e6 fixed warning, turned of -Werror for fortran to try and get github workflow building 3b63878 fixed warning, turned of -Werror for fortran to try and get github workflow building fb4052a turning on -Wall for strict autotools build aa9f62c turning on -Wall for strict autotools build 1085b95 Merge branch 'master' into ejh_next_9 23c5c50 Merge pull request #1726 from jedwards4b/reduce_search_netcdf 43f1315 remove more redundant find_package calls 6526724 add space cc11af9 no netcdf fortran in this test 8b97bd5 remove debug print statements 57f939f only search for netcdf at top level fe2fb7a removed extra workflow for now 5acda4b error out of cmake if netcdf-c dispatch table wont work for netcdf integration 52367bd trying to add another workflow a043a91 trying to add another workflow 9be18ae took comments out of workflow file b26239d adding netCDF interation to build summary and pio_meta.h f1a83f3 Merge pull request #1715 from NCAR/ejh_ncint e57c5aa properly dealing with ncint_mod.F90 in cmake build 78dd092 clean up 15527bf cleaned up cmake_config.h.in a604f76 added new github workflow for netCDF integration with cmake 08c7999 now all ncint tests work 444f023 more work on ncint in cmake build 6bd5fa4 moved cmake build of ncint into src/clib dir, now test works! 9f57a5c ncint build working! eaa0656 now building ncint directory with cmake cab47c3 merged changes from master a59a55b Merge pull request #1722 from NCAR/ejh_next_7 a1a04ef moved .f90 to .F90 089a7ec turning off logging in a test 5b7f801 more fortran flag cleanup 5f190e8 more fortran flag cleanup 7067c63 cleanup of flags in test/unit autotools build 4d6e4f8 more flag cleanup a91eed9 more flag cleanup db93ea5 more changes so that all fortran files use config.h 0a10f86 adding some cmakedefines 6213867 cleanup of flag use in src/flib 4f80a53 Merge pull request #1720 from NCAR/ejh_next_6 0b2bebe removed unneeded pre-processor symbol from cmake_config.h.in 9b942c5 Merge pull request #1719 from NCAR/ejh_next_5 b258478 removed troublesome strnlen() function 85edfb8 removed more unneeded pre-processor stuff 1ac844f removed more unneeded pre-processor stuff 8a82dea removed more unneeded pre-processor stuff 8a8ba30 more removal of unneeded pre-processor symbols 4754ab5 removed unneeded check of _NETCDF ad4eddb removed NETCDF flag c99eb28 Merge pull request #1718 from NCAR/ejh_next_3 4430bcd changed build summary 2676343 clean up travis file 7153ec9 removed constant 084f1c1 Merge pull request #1716 from NCAR/ejh_next 90d9af6 removed config constant that is unused anywhere... f269769 fixed setting of configure define in cmake b38aaef starting to add ncint code to cmake build a28ec8c fixing cmake use of defines c5794a8 trying to fix cmake build 768c0c4 merged master a9ed7f1 Merge pull request #1714 from NCAR/ejh_fix_cmake_2 b985532 fixed creation of config.h on read-only filesystem 52ac327 adding support for NETCDF_INTEGRATION option to cmake, also fixing cmake build issue in read-only directories 116cd6e Merge pull request #1710 from NCAR/ejh_cmake_fix 0300688 including HAVE_PAR_FILTERS in cmake config.h eed7d48 Merge pull request #1707 from NCAR/ejh_cache_2 c0aa71a now trying caching for cmake build fc96bb3 now trying caching for cmake build 6d93e73 now trying caching for cmake build 359bc44 now trying caching for cmake build 9b46b90 now trying caching for cmake build e307f96 now trying caching for strict pnetcdf build ab5f234 now trying caching for pnetcdf build 7e40029 now trying caching for pnetcdf build e11337c now install pnetcdf in subdirectory 2376632 Merge pull request #1705 from NCAR/ejh_fix_makefile 658b209 fixed makefile 9d4dbb7 Merge pull request #1700 from NCAR/ejh_4_7_2 ce1828a took out caching attempt 09a7b2c added comment bb3fc14 cmake determination of par filters presence 5e51323 attempting to cache pnetcdf build in workflow 3482946 changed fortran test to ignore deflate tests on NETCDF4P iotype f591b8c now use HAVE_PAR_FILTERS in test_pioc.c 8a298dc now check for netcdf-c disptach version in autoconf and cmake f66d558 fixed detection of 4.7.2 in autoconf to work for old netcdf releases that don't have netcdf_meta.h 042ea81 added nc-config output to travis 3f45048 added nc-config output to travis e049af4 added nc-config output to travis 8ac93fe added nc-config output to travis 783ff4d added nc-config output to travis 4ed861e added nc-config output to travis e0eb090 disallow netcdf-c-4.7.2 for both cmake and autotools builds a14b65b Merge pull request #1698 from NCAR/ejh_test_simple ee339d0 fixed cmake running on 4 procs 62d09ee called MPI_Finalize() in test_simple.c 8f40a3a cleaned up simple test 39d4c79 merged master eedc46c Merge pull request #1696 from NCAR/ejh_fix_test_leak 4438bf5 turns out we need fortran for pnetcdf 28fcb48 turn off cxx and fortran for pnetcdf build 56243cf turn off netcdf-integration in travis testing 88cf3d1 turn on netcdf-integration in travis testing abef381 fixed memory leaks in tests 64a117c Merge pull request #1690 from NCAR/ejh_docs_2 e663bf3 removing redundant build 05ad86b turning on fortran build for autotools 90a1a20 turning on fortran build for autotools 0876585 turning on fortran build for autotools dd9d7dd trying doc build a different way 0cdc421 trying doc build a different way 0e6e349 trying doc build a different way 282e338 now can turn on deflate with netcdf-4 parallel e7cdd55 got working for current state of play 3d4b09e now reading and checking data aee02f3 getting test_simple working a430197 getting test_simple working 09965b8 added unlimited dim, also creating decomp 137db07 now creating dim and var in test_simple 0c15892 starting to fill in test_simple 56ea154 developing simple test 958d9b9 added test_simple.c git-subtree-dir: src/externals/pio2 git-subtree-split: 76c40a7855c99403bfd9e3dee9062c7fe58b4391

kdraeder assigned billsacks and bertinia Sep 22, 2017

rljacob added the in progress label Sep 22, 2017

kdraeder requested review from billsacks, bertinia and jedwards4b September 22, 2017 22:48

kdraeder added 2 commits September 22, 2017 17:08

Committing all changes, may want to undo some.

dd87719

Just for testing.

jedwards4b force-pushed the kdraeder/fix_st_archive branch from 8c77f31 to 1c2446f Compare September 22, 2017 23:09

jedwards4b reviewed Sep 22, 2017

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jedwards4b requested changes Sep 22, 2017

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billsacks requested changes Sep 23, 2017

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bertinia reviewed Sep 26, 2017

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resolved merge conflicts. Also responded to comments

5eef510

jedwards4b requested changes Sep 26, 2017

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rljacob added tp: CIMElib ty: Bug Fix labels Sep 26, 2017

billsacks mentioned this pull request Sep 27, 2017

scripts_regression_tests should set up a temporary directory for testing baseline generation #1928

Closed

Re-introducing changes based on reviews of first push. There were 2 f…

7ac36e3

…ailures in scripts_regression_tests.py, but probably not related to case_st_archive.py changes.

billsacks mentioned this pull request Sep 27, 2017

Logic in case_st_archive doesn't allow multi-instance cases with mpas components #1931

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billsacks requested changes Sep 27, 2017

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Removed outdated debugging statement and 2 lines of redundant code.

8ea228a

jedwards4b approved these changes Sep 28, 2017

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billsacks approved these changes Sep 28, 2017

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bertinia approved these changes Sep 28, 2017

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billsacks merged commit 874dc10 into master Sep 28, 2017

billsacks removed the in progress label Sep 28, 2017

kdraeder deleted the kdraeder/fix_st_archive branch September 28, 2017 22:05

Kdraeder/fix st archive #1916

Kdraeder/fix st archive #1916

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billsacks commented Sep 27, 2017

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