update GAMESS-US easyblock to directly write install.info #2791

sassy-crick · 2022-09-22T13:23:39Z

(created using eb --new-pr)

…ilders#1925

sassy-crick · 2022-09-22T13:35:21Z

This is a working EasyBlock for recent releases of GAMESS-US releases.
The idea is instead of doing the question-and-answer bit, simply provide a install.info, which is the result of the Q&A session anyway. I tried to build GAMESS-US in such a way where I know it is working on a cluster using sockets. Using mpi should work as well but I did not test that. I have tried to include other features like OpenMP which works, but I have not really done any work with for example libxc. I only tried that briefly using the EB libxc but that did not pan out during the build step so I left it out. I done some bug-catching for mkl as the older compall scripts don't have the oneapi feature.
There is probably room for improving my Python, no doubt, and also room to add more to it. I fixed setting the maximum number of cores/nodes for ddikick.x so it can be set in the EasyConfig file, where OpenMPI can be turned off as well so required.
Nice to have:

get libxc working
get OpenBLAS-64 working
CUDA?
change to use make instead of the compall script?

hound · 2022-09-22T15:34:19Z

easybuild/easyblocks/g/gamess_us.py

+                line = re.sub(r"(null\) set VERNO)=.*", r"\1=%s" % self.version, line)
+                line = re.sub(r"^(\s*set DDI_MPI_CHOICE)=.*", r"\1=%s" % mpilib, line)
+                line = re.sub(r"^(\s*set DDI_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)
+                line = re.sub(r"^(\s*set GA_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)


undefined name 'mpilib'
undefined name 'mpilib_path'

hound · 2022-09-22T15:34:19Z

easybuild/easyblocks/g/gamess_us.py

+                line = re.sub(r"^(\s*set\s*GMS_OPENMP)=.*", r"\1=%s" % "true", line) # changed in gamess-20190930-R2 for OpenBLAS support
+                line = re.sub(r"(null\) set VERNO)=.*", r"\1=%s" % self.version, line)
+                line = re.sub(r"^(\s*set DDI_MPI_CHOICE)=.*", r"\1=%s" % mpilib, line)
+                line = re.sub(r"^(\s*set DDI_MPI_ROOT)=.*%s.*" % mpilib.lower(), r"\1=%s" % mpilib_path, line)


undefined name 'mpilib'
undefined name 'mpilib_path'

hound · 2022-09-22T15:34:19Z

easybuild/easyblocks/g/gamess_us.py

+                line = re.sub(r"^(\s*set\s*GMSPATH)=.*", r"\1=%s\n%s" % (self.installdir, extra_gmspath_lines), line)
+                line = re.sub(r"^(\s*set\s*GMS_OPENMP)=.*", r"\1=%s" % "true", line) # changed in gamess-20190930-R2 for OpenBLAS support
+                line = re.sub(r"(null\) set VERNO)=.*", r"\1=%s" % self.version, line)
+                line = re.sub(r"^(\s*set DDI_MPI_CHOICE)=.*", r"\1=%s" % mpilib, line)


undefined name 'mpilib'

hound · 2022-09-22T15:34:19Z

easybuild/easyblocks/g/gamess_us.py

+            for line in fileinput.input(rungms, inplace=1, backup='.orig'):
+                line = re.sub(r"^(\s*set\s*TARGET)=.*", r"\1=%s" % self.cfg['ddi_comm'], line)
+                line = re.sub(r"^(\s*set\s*GMSPATH)=.*", r"\1=%s\n%s" % (self.installdir, extra_gmspath_lines), line)
+                line = re.sub(r"^(\s*set\s*GMS_OPENMP)=.*", r"\1=%s" % "true", line) # changed in gamess-20190930-R2 for OpenBLAS support


at least two spaces before inline comment
line too long (137 > 120 characters)

hound · 2022-09-22T15:34:20Z

easybuild/easyblocks/g/gamess_us.py

+                raise EasyBuildError("Failed to patch actvte.code", actvte, err)
+            # compiling
+            run_cmd("mv %s/tools/actvte.code" % self.builddir + " %s/tools/actvte.f" % self.builddir)
+            run_cmd("%s -o " % fortran_comp + " %s/tools/actvte.x" % self.builddir + " %s/tools/actvte.f" % self.builddir)


line too long (122 > 120 characters)

hound · 2022-09-22T15:34:21Z

easybuild/easyblocks/g/gamess_us.py

-            "Enter your choice of 'mkl' or .* 'none': ": mathlib,
-        }
-        run_cmd_qa(cmd, qa=qa, std_qa=stdqa, log_all=True, simple=True)
+        f.writelines(["setenv GMS_MPI_LIB " + mpilib + "\n" + 


trailing whitespace

hound · 2022-09-22T15:34:21Z

easybuild/easyblocks/g/gamess_us.py

        # verify selected DDI communication layer
        known_ddi_comms = ['mpi', 'mixed', 'shmem', 'sockets']
        if not self.cfg['ddi_comm'] in known_ddi_comms:
            raise EasyBuildError("Unsupported DDI communication layer specified (known: %s): %s",
                                 known_ddi_comms, self.cfg['ddi_comm'])
+
+        f.writelines(["setenv GMS_DDI_COMM " + self.cfg['ddi_comm'] + "\n" ])


whitespace before ']'

hound · 2022-09-22T15:34:21Z

easybuild/easyblocks/g/gamess_us.py

        # verify selected DDI communication layer
        known_ddi_comms = ['mpi', 'mixed', 'shmem', 'sockets']
        if not self.cfg['ddi_comm'] in known_ddi_comms:
            raise EasyBuildError("Unsupported DDI communication layer specified (known: %s): %s",
                                 known_ddi_comms, self.cfg['ddi_comm'])
+


blank line contains whitespace

hound · 2022-09-22T15:34:21Z

easybuild/easyblocks/g/gamess_us.py

+        f.writelines(["setenv GMS_MATHLIB " + mathlib + "\n" +
+            "setenv GMS_MATHLIB_PATH " + mathlib_root + "\n" +
+            "setenv GMS_MKL_VERNO " + mathlib_vers + "\n" +
+            "setenv GMS_LAPACK_LINK_LINE" + "" + "\n"])


continuation line under-indented for visual indent

hound · 2022-09-22T15:34:21Z

easybuild/easyblocks/g/gamess_us.py

        else:
            mathlib = mathlib.lower()

+        f.writelines(["setenv GMS_MATHLIB " + mathlib + "\n" +
+            "setenv GMS_MATHLIB_PATH " + mathlib_root + "\n" +
+            "setenv GMS_MKL_VERNO " + mathlib_vers + "\n" +


continuation line under-indented for visual indent

saromleang · 2022-09-22T15:58:33Z

Have a look at ./bin/create-install-info.py --help within the GAMESS directory. We use for our internal continuous integration.

sassy-crick · 2022-09-26T10:50:52Z

Have a look at ./bin/create-install-info.py --help within the GAMESS directory. We use for our internal continuous integration.

@saromleang Thanks for pointing that out to us! That looks promising. Just to confirm: any changes to the ''install.info'' script will be taken care of by running that command.So if a new field is added, the script will be automatically updated. Is that correct?

saromleang · 2022-09-28T08:43:05Z

Have a look at ./bin/create-install-info.py --help within the GAMESS directory. We use for our internal continuous integration.

@saromleang Thanks for pointing that out to us! That looks promising. Just to confirm: any changes to the ''install.info'' script will be taken care of by running that command.So if a new field is added, the script will be automatically updated. Is that correct?

Yes, we have a document template for install.info that is leverage by ./bin/create-install-info.py that keeps up with any changes to fields in install.info. Just be aware that ./bin/create-install-info.py does not handle all targets (e.g., hpe-cray-ex). But the most common target linux64 should be fully support along with build options under linux64.

Micket

Please do something along the lines of

buildopts = dict()
...
buildopts['VB2000'] = self.cfg['use_bundled_vb2000']
...
for key, val in buildopts.items():
    f.write('setenv', key, val, '\n')

lexming

I really like this approach of directly writing install.info instead going through the question/answer game. However there are several parts of the easyblock that need improvement.

I've been carefully reviewing the code of this easyblock and I made extensive changes to it that address the main problems outlined below. Please check my changes in sassy-crick#1 and if you agree with them merge it to this PR.

lexming · 2023-03-07T10:38:57Z

easybuild/easyblocks/g/gamess_us.py

        else:
            mathlib = mathlib.lower()

+        f.writelines(["setenv GMS_MATHLIB " + mathlib + "\n" +
+            "setenv GMS_MATHLIB_PATH " + mathlib_root + "\n" +
+            "setenv GMS_MKL_VERNO " + mathlib_vers + "\n" +


mathlib_vers is not necessarily assigned here, you only defined it for imkl

lexming · 2023-03-07T14:05:18Z

easybuild/easyblocks/g/gamess_us.py

+            run_cmd("mv %s/tools/actvte.code" % self.builddir + " %s/tools/actvte.f" % self.builddir)
+            run_cmd("%s -o " % fortran_comp + " %s/tools/actvte.x" % self.builddir + " %s/tools/actvte.f" % self.builddir)
+
+    def build_step(self):


you are adding a second build_step here, I guess it's leftover code.

lexming · 2023-03-07T15:01:32Z

easybuild/easyblocks/g/gamess_us.py

@@ -64,6 +67,7 @@ def extra_options():
            'maxcpus': [None, "Maximum number of cores per node", MANDATORY],
            'maxnodes': [None, "Maximum number of nodes", MANDATORY],
            'runtest': [True, "Run GAMESS-US tests", CUSTOM],
+            'omp': [False, "Enabling OpenMP", CUSTOM],


this can be replaced with toolchain.options.openmp

lexming · 2023-03-11T23:04:55Z

easybuild/easyblocks/g/gamess_us.py

 from easybuild.tools.modules import get_software_root, get_software_version
+from easybuild.tools.py2vs3 import ascii_letters
 from easybuild.tools.run import run_cmd, run_cmd_qa


run_cmd_qa is no longer needed

lexming · 2023-03-11T23:13:30Z

easybuild/easyblocks/g/gamess_us.py

@@ -88,12 +94,17 @@ def extract_step(self):

    def configure_step(self):
        """Configure GAMESS-US build via provided interactive 'config' script."""
-
+        """Opening install.info file as append"""
+        f = open(self.builddir + "/install.info", "a")


you can leverage write_file from easybuild instead of manually opening and closing the file handler

akesandgren · 2023-09-11T10:43:46Z

@sassy-crick ping on this one...

lexming · 2023-12-14T11:50:03Z

@sassy-crick your commits are now part of #3047 where we are continuing this PR.

Closing as superseded by #3047

Working EasyBlock for newer versions of GAMESS-US, based on PR easybu…

b520b2e

…ilders#1925

sassy-crick mentioned this pull request Sep 22, 2022

{chem}[gomkl/2020a,gomkl/2021a] GAMESS-US v20200630-R1, GAMESS-US v20200930-R2, GAMESS-US v20210620-R1, ... easybuilders/easybuild-easyconfigs#16291

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hound bot reviewed Sep 22, 2022

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Micket requested changes Sep 28, 2022

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boegel added the update label Oct 4, 2022

boegel added this to the 4.x milestone Oct 4, 2022

boegel changed the title ~~Working EasyBlock for newer versions of GAMESS-US, based on PR #1925~~ update GAMESS-US easyblock for newer versions Oct 12, 2022

lexming mentioned this pull request Mar 13, 2023

multiple fixes for PR easybuilders#2791 sassy-crick/easybuild-easyblocks#1

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lexming requested changes Mar 13, 2023

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lexming changed the title ~~update GAMESS-US easyblock for newer versions~~ update GAMESS-US easyblock to directly write install.info Mar 13, 2023

lexming closed this Dec 14, 2023

lexming mentioned this pull request Dec 18, 2023

refactor GAMESS-US easyblock to directly write install.info #3047

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lexming modified the milestones: 4.x, next release (4.9.0?) Dec 18, 2023

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update GAMESS-US easyblock to directly write install.info #2791

update GAMESS-US easyblock to directly write install.info #2791

sassy-crick commented Sep 22, 2022

sassy-crick commented Sep 22, 2022 •

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update GAMESS-US easyblock to directly write install.info #2791

update GAMESS-US easyblock to directly write install.info #2791

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