Moose Installation - HPC

[normjona]

Hi,

I'm installing moose and BISON on an HPC cluster and have been running into what appears to be a libmesh related error.

After successfully running the update and rebuild PETSc script, I run run the update and rebuild libmesh script. I get this error

---------------------------------------------
-- Done configuring core library features ---
---------------------------------------------
---------------------------------------------
----- Configuring for optional packages -----
---------------------------------------------
checking for built-in XDR support... no
checking for XDR support in /usr/include/tirpc... no
configure: error: *** XDR was not found, but --enable-xdr-required was specified.
Running make -j 1...
make: *** No targets specified and no makefile found.  Stop.

After this when I try to run the make command, I get the following errors.

make -j 4
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/libtool: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Traceback (most recent call last):
  File "/nfs/home/jnorma18/projects/moose/framework/scripts/get_repo_revision.py", line 19, in <module>
    from packaging import version
ModuleNotFoundError: No module named 'packaging'
Checking if header needs updating: /nfs/home/jnorma18/projects/moose/framework/include/base/MooseRevision.h...
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
Compiling C++ (in opt mode) /nfs/home/jnorma18/projects/moose/framework/build/unity_src/src_Unity.C...
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/contrib/bin/libmesh-config: No such file or directory
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/libtool: No such file or directory
Compiling C++ (in opt mode) /nfs/home/jnorma18/projects/moose/framework/build/unity_src/actions_Unity.C...
make: *** [/nfs/home/jnorma18/projects/moose/framework/build.mk:144: /nfs/home/jnorma18/projects/moose/framework/build/unity_src/src_Unity..opt.lo]
 Error 127
make: *** Waiting for unfinished jobs....
/bin/sh: /nfs/home/jnorma18/projects/moose/libmesh/installed/libtool: No such file or directory
make: *** [/nfs/home/jnorma18/projects/moose/framework/build.mk:145: /nfs/home/jnorma18/projects/moose/framework/build/unity_src/actions_Unity..opt
.lo] Error 127

My libmesh directory isn't including the "install" directory. It seems libmesh is failing to build correctly? I'd appreciate any help on this.

Thanks,
Jonathan Norman

[GiudGiud]

hello

Libmesh did not build properly.
The moose error you got afterwards is 'libmesh not installed' basically
You need to install this library on your cluster libtirpc-devel then try to install libmesh again

Guillaume

[echo1115]

Thanks for your reply @roystgnr
Actually, I need to offline install MOOSE on a RHEL 8.4 cluster. When encountering the configure error for libmesh, I run this:

[dcq@localhost ~]$ rpm -q libtirpc
libtirpc-1.1.4-4.el8.x86_64

indicating that libtirpc is already packaged via rpm in the system, but libtirpc-devel is missing. Then I downloaded the libtirpc-devel rpm package suitable for CentOS 8 from this website: link, but I'm unable to install the 'libtirpc-devel-1.1.4-5.el8.x86_64.rpm' to the directory I want.

Regarding the link you provided:

You might be stuck installing from source. Looks like the official git repo is at https://git.linux-nfs.org/?p=steved/libtirpc.git;a=summary and 1.3.4 is the latest release version.

I assume it's for installing libtirpc rather than libtirpc-devel.

[roystgnr]

indicating that libtirpc is already packaged via rpm in the system, but libtirpc-devel is missing

Wait, your sysadmin said he didn't want to install the headers used to compile against already-installed libraries in order to avoid conflicts with other software? That's ... a philosophy, I guess? Pity the poor developers like you who have to install their own TIRPC to get it work and then also have to make sure it's either ABI-compatible with or not conflicting with the system version.

The link I provided is for all of TIRPC, which is both tirpc and tirpc-devel. RedHat breaks these packages into multiple different rpms, so that end users can install the parts (e.g. libraries, in the tirpc .rpm) needed to run already-compiled programs without having to also install the parts (e.g. header files, in the tirpc-devel .rpm) needed to compile new programs. Ideally you'd simply build all of TIRPC yourself and link against it... but if the TIRPC rpm is already installed you'll need to either keep its (system!) library directory out of your linker path, or you'll have to get the version matching the tirpc version that's installed, cross your fingers hoping there aren't any ABI-incompatible patches on that rpm's version, and use the headers you download to link to the libraries already installed.

[echo1115]

@roystgnr Thank you for detailed explanation and sharing your guidance on this matter.
Now I've decided to proceed with installing TIRPC from the source code provided in the link you shared. During the process, I've encountered many missing packages in my system, such as autoconf, automake, libtool, and others. Similarly, I'll need to install them from source code, and to install them, I need to install additional tools or modules. It feels like a never-ending process, and I'm unsure where it ends. However, I hope that this will eventually lead to successfully installing TIRPC, enabling me to proceed with compiling and rebuilding libmesh.

[milljm]

For these types of dependencies, I like to use a clean Conda environment to satisfy.

1. Install Conda
2. Create a pristine environment, purposefully only containing what is necessary (whats missing from the System):

conda create -n libmesh-dependencies libxt-devel-cos7-x86_64=1.1.5
conda activate libmesh-dependencies

And then try to run ./update_and_rebuild_libmesh.sh again. The above should take care of libtirpc.

Upon the next error (if there is any), install that one single requirement while in the libmesh-dependencies Conda environment, and try again. Repeat.

If memory serves, you might run into the next set of missing 'things'. Do not install unless necessary!

autoconf
automake
m4
libtool    # I would hope not

[echo1115]

@milljm Thank you for your suggestion! It is also a good idea