Installing on HPC - error in make #32078

rnpratoori · 2025-12-11T15:07:36Z

rnpratoori
Dec 11, 2025

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Issue or question about MOOSE

I am installing MOOSE on HPC. The execution of petsc, libmesh and wasp completed without errors. But when running make -j6 inside moose/test gives errors

Compiling C++ (in opt mode) /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/unity_src/partitioner_Unity.C...
In file included from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/MooseTypes.h:12,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/MooseUtils.h:13,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/MooseObject.h:13,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/MoosePartitioner.h:13,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/PetscExternalPartitioner.h:14,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/BlockWeightedPartitioner.h:12,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/src/partitioner/BlockWeightedPartitioner.C:10,
                 from /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/unity_src/partitioner_Unity.C:2:
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:273:1: error: 'MPI_Comm' does not name a type
  273 | MPI_Comm swapLibMeshComm(MPI_Comm new_comm);
      | ^~~~~~~~
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:280:29: error: expected ')' before 'new_comm'
  280 |   ScopedCommSwapper(MPI_Comm new_comm) : _orig(swapLibMeshComm(new_comm)) {}
      |                    ~        ^~~~~~~~~
      |                             )
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:289:3: error: 'MPI_Comm' does not name a type
  289 |   MPI_Comm _orig;
      |   ^~~~~~~~
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h: In destructor 'virtual Moose::ScopedCommSwapper::~ScopedCommSwapper()':
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:281:50: error: '_orig' was not declared in this scope
  281 |   virtual ~ScopedCommSwapper() { swapLibMeshComm(_orig); }
      |                                                  ^~~~~
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:281:34: error: 'swapLibMeshComm' was not declared in this scope
  281 |   virtual ~ScopedCommSwapper() { swapLibMeshComm(_orig); }
      |                                  ^~~~~~~~~~~~~~~
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h: In member function 'void Moose::ScopedCommSwapper::forceSwap()':
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:286:22: error: '_orig' was not declared in this scope
  286 |   void forceSwap() { _orig = swapLibMeshComm(_orig); }
      |                      ^~~~~
/work/mech-ai/rnp/MOOSE/projects/moose/framework/build/header_symlinks/Moose.h:286:30: error: 'swapLibMeshComm' was not declared in this scope
  286 |   void forceSwap() { _orig = swapLibMeshComm(_orig); }
      |                              ^~~~~~~~~~~~~~~
make: *** [/work/mech-ai/rnp/MOOSE/projects/moose/framework/build.mk:167: /work/mech-ai/rnp/MOOSE/projects/moose/framework/build/unity_src/partitioner_Unity.x86_64-pc-linux-gnu.opt.lo] Error 1

(Optional) code in question / simulation log / errors

No response

Encountering Errors? Please include diagnostic output

####################################################################################################
Influential Environment Variables

APPTAINER_BINDPATH=/work:/work,/lustre:/lustre,/scratch:/scratch,/ptmp:/ptmp,/etc/hosts:/etc/hosts
APPTAINER_CACHEDIR=/tmp
APPTAINER_TMPDIR=/tmp
CC=mpicc
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CURL_CA_BUNDLE=
CXX=mpicxx
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F90=mpif90
FC=mpif90
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SLURM_JOB_UID=407477
SLURM_JOB_USER=rnp
SLURM_LAUNCH_NODE_IPADDR=172.16.4.2
SLURM_LOCALID=0
SLURM_MEM_PER_NODE=262144
SLURM_MPI_TYPE=pmix
SLURM_NNODES=1
SLURM_NODEID=0
SLURM_NODELIST=nova18-wide-26
SLURM_NPROCS=8
SLURM_NTASKS=8
SLURM_OOM_KILL_STEP=0
SLURM_PMIX_MAPPING_SERV=(vector,(0,1,1))
SLURM_PMIXP_ABORT_AGENT_PORT=40367
SLURM_PRIO_PROCESS=0
SLURM_PROCID=0
SLURM_PTY_PORT=33669
SLURM_PTY_WIN_COL=183
SLURM_PTY_WIN_ROW=50
SLURM_SCRIPT_CONTEXT=prolog_task
SLURM_SRUN_COMM_HOST=172.16.4.2
SLURM_SRUN_COMM_PORT=36139
SLURM_STEP_ID=4294967290
SLURM_STEPID=4294967290
SLURM_STEP_LAUNCHER_PORT=36139
SLURM_STEP_NODELIST=nova18-wide-26
SLURM_STEP_NUM_NODES=1
SLURM_STEP_NUM_TASKS=1
SLURM_STEP_TASKS_PER_NODE=1
SLURM_SUBMIT_DIR=/work/mech-ai/rnp/MOOSE/projects
SLURM_SUBMIT_HOST=nova-login-2
SLURM_TASK_PID=3425519
SLURM_TASKS_PER_NODE=8
SLURM_TOPOLOGY_ADDR=nova18-wide-26
SLURM_TOPOLOGY_ADDR_PATTERN=node
SSL_CERT_FILE=
####################################################################################################
Compiler(s) (CC CXX FC F77 F90):

which $CC; /opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/bin/mpicc
$CC --version; gcc (GCC) 11.4.1 20231218 (Red Hat 11.4.1-4)
$CC -show; /usr/bin/gcc -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -L/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -Wl,-rpath -Wl,/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpi

which $CXX; /opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/bin/mpicxx
$CXX --version; g++ (GCC) 11.4.1 20231218 (Red Hat 11.4.1-4)
$CXX -show; /usr/bin/g++ -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -L/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpicxx -Wl,-rpath -Wl,/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpi

which $FC; /opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/bin/mpif90
$FC --version; GNU Fortran (GCC) 11.4.1 20231218 (Red Hat 11.4.1-4)
$FC -show; /usr/bin/gfortran -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -L/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpifort -Wl,-rpath -Wl,/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpi

which $F77; /opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/bin/mpif77
$F77 --version; GNU Fortran (GCC) 11.4.1 20231218 (Red Hat 11.4.1-4)
$F77 -show; /usr/bin/gfortran -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -L/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpifort -Wl,-rpath -Wl,/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpi

which $F90; /opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/bin/mpif90
$F90 --version; GNU Fortran (GCC) 11.4.1 20231218 (Red Hat 11.4.1-4)
$F90 -show; /usr/bin/gfortran -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -I/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/include -L/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpifort -Wl,-rpath -Wl,/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/mpich-4.1.1-7i44p3xpqces2nujej5hjbnxopb4p7mp/lib -lmpi

OK
####################################################################################################
Python Sanity Checks

/usr/bin/env python3 --version; (reporting as: Python 3.10.10) matches
which python3 python;

/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/python-3.10.10-zwlkg4ljdinozolpn7os3bpbjvu7sw6m/bin/python3 --version; == Python 3.10.10
/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/python-3.10.10-zwlkg4ljdinozolpn7os3bpbjvu7sw6m/bin/python --version; == Python 3.10.10

OK
####################################################################################################
Python Modules (TestHarness, run-ability)

OK


checks PASSED

Answered by GiudGiud

Dec 15, 2025

ok I recall that in the past we have needed libtirpc-devel not just libtirpc.
Can you check if that first package is available on your system somewhere?
Can you attach the config.log as well?

Also I think you can achieve what you want to do without XDR, but using the XDA xda.gz files instead. They don't require xdr

View full answer

GiudGiud · 2025-12-11T15:53:08Z

GiudGiud
Dec 11, 2025
Collaborator

hello

which instructions are you following?
and you change anything about the environment between compiling libmesh and MOOSE?

1 reply

rnpratoori Dec 11, 2025
Author

I followed the instructions here - https://mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html

I don't think I have changed anything. I loaded the modules I used and set mpi* variables.

 module load python/3.10.10-zwlkg4l gcc/12.2.0-khmr45w cmake/3.27.4       py-packaging/23.0-py310-uqu2hz3 py-pyyaml/6.0-py310-iiufst2         py-jinja2/3.1.2-py310-qkbkwne mpich/4.1.1-py310-7i44p3x           py-numpy/1.26.3-py310-gntgk2n py-setuptools/67.6.0-py310-kxkl7ol libtirpc/1.2.6-5lcsktv

export CC=mpicc CXX=mpicxx FC=mpif90 F90=mpif90 F77=mpif77

rnpratoori · 2025-12-12T18:16:33Z

rnpratoori
Dec 12, 2025
Author

@GiudGiud I did a clean install again and it worked. I wanted to split the mesh and I got this error -


*** ERROR ***
The following occurred in the main Application of type pantherTestApp.

ERROR: Functionality is not available.
Make sure LIBMESH_HAVE_XDR is defined at build time
The XDR interface is not available in this installation
Stack frames: 15
0: libMesh::print_trace(std::ostream&)
1: libMesh::MacroFunctions::report_error(char const*, int, char const*, char const*, std::ostream&)
2: libMesh::Xdr::open(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >)
3: libMesh::Xdr::Xdr(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, libMesh::XdrMODE)
4: libMesh::CheckpointIO::write(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
5: SplitMeshAction::act()
6: Action::timedAct()
7: ActionWarehouse::executeActionsWithAction(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)
8: ActionWarehouse::executeAllActions()
9: MooseApp::runInputFile()
10: MooseApp::run()
11: main
12: /lib64/libc.so.6(+0x29590) [0x14f484c71590]
13: __libc_start_main
14: /work/mech-ai/rnp/MOOSE/projects/panther/panther-opt() [0x407615]
[0] ../src/utils/xdr_cxx.C, line 187, compiled Dec 11 2025 at 22:44:51

I have removed --enable-xdr-required and used --with-xdr-include=PATH along with a libtirpc module loaded. What am I missing here?

5 replies

GiudGiud Dec 12, 2025
Collaborator

I have removed --enable-xdr-required

you should not need to do that. Removing is what allowed you to build without XDR, hence the issue

--with-xdr-include=PATH along with a libtirpc module loaded

what path did you use?

Did you try --with-xdr-libdir=/foo/bar

rnpratoori Dec 12, 2025
Author

I used the path for libtirpc/lib. I did not try --with-xdr-libdir=/foo/bar. What directory should I point it to? libtirpc?

rnpratoori Dec 13, 2025
Author

I turned on --enable-xdr-required and I tried with and without --with-xdr-libdir and --with-xdr-libname. All were giving me the error message - configure: error: *** XDR was not found, but --enable-xdr-required was specified.

These were the options I used:

 --enable-xdr-required \
               --with-xdr-include=/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/libtirpc-1.2.6-5lcsktvzdn3r65t5o22ajudbaxhckmfz/include/tirpc/rpc \
               --with-xdr-libdir=/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/libtirpc-1.2.6-5lcsktvzdn3r65t5o22ajudbaxhckmfz/lib \
               --with-xdr-libname=/opt/rit/el9/20230413/app/linux-rhel9-x86_64_v3/gcc-11.2.1/libtirpc-1.2.6-5lcsktvzdn3r65t5o22ajudbaxhckmfz/lib/libtirpc.so \

I need XDR because I want to split my mesh for better scaling. Is there any other way I can do it?

GiudGiud Dec 15, 2025
Collaborator

ok I recall that in the past we have needed libtirpc-devel not just libtirpc.
Can you check if that first package is available on your system somewhere?
Can you attach the config.log as well?

Also I think you can achieve what you want to do without XDR, but using the XDA xda.gz files instead. They don't require xdr

Answer selected by rnpratoori

rnpratoori Dec 18, 2025
Author

I just shifted to using xda.

Installing on HPC - error in make #32078

Uh oh!

rnpratoori Dec 11, 2025

Check these boxes if you have followed the posting rules.

Issue or question about MOOSE

(Optional) code in question / simulation log / errors

Encountering Errors? Please include diagnostic output

Replies: 2 comments · 6 replies

Uh oh!

GiudGiud Dec 11, 2025 Collaborator

Uh oh!

rnpratoori Dec 11, 2025 Author

Uh oh!

Uh oh!

rnpratoori Dec 12, 2025 Author

Uh oh!

GiudGiud Dec 12, 2025 Collaborator

Uh oh!

rnpratoori Dec 12, 2025 Author

Uh oh!

Uh oh!

rnpratoori Dec 13, 2025 Author

Uh oh!

Uh oh!

GiudGiud Dec 15, 2025 Collaborator

Uh oh!

rnpratoori Dec 18, 2025 Author

rnpratoori
Dec 11, 2025

Replies: 2 comments 6 replies

GiudGiud
Dec 11, 2025
Collaborator

rnpratoori Dec 11, 2025
Author

rnpratoori
Dec 12, 2025
Author

GiudGiud Dec 12, 2025
Collaborator

rnpratoori Dec 12, 2025
Author

rnpratoori Dec 13, 2025
Author

GiudGiud Dec 15, 2025
Collaborator

rnpratoori Dec 18, 2025
Author