Intel installation issue

[Jordi Sanglas Molist]

Hi all,

I was trying to install PETSc and PFLOTRAN using Intel compilers on Linux, but I have some issues.

After cloning PETSc, I run the following configuration command:

./configure --CFLAGS=-O3 --CXXFLAGS=-O3 --FFLAGS=-O3 --with-debugging=no --download-hdf5=yes --download-fblaslapack=yes --download-ptscotch=yes --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90

I verified that mpicc, mpicxx and mpif90 have the correct paths (by using which mpif90, which mpicc...). Then I use the command make all and PETSc is compiled successfully. However, after running the PETSc tests using make check, one of them fails:

Running check examples to verify correct installation

Using PETSC_DIR=/home/altopt/intel_pflotran/petsc and PETSC_ARCH=arch-linux2-c-opt

C/C++ example src/snes/tutorials/ex19 run successfully with 1 MPI process

Possible error running C/C++ src/snes/tutorials/ex19 with 2 MPI processes

See http://www.mcs.anl.gov/petsc/documentation/faq.html

[1625044409.741787] [ord-19-18:87818:0]         select.c:406  UCX  ERROR no remote registered memory access transport to <no debug data>: self/self - Destination is unreachable, mm/sysv - Destination is unreachable, mm/posix - Destination is unreachable, cma/cma - no put short

[1625044409.741824] [ord-19-18:87817:0]         select.c:406  UCX  ERROR no remote registered memory access transport to <no debug data>: self/self - Destination is unreachable, mm/sysv - Destination is unreachable, mm/posix - Destination is unreachable, cma/cma - no put short

Abort(1091215) on node 1 (rank 1 in comm 0): Fatal error in PMPI_Init_thread: Other MPI error, error stack:

MPIR_Init_thread(138)........: 

MPID_Init(1139)..............: 

MPIDI_OFI_mpi_init_hook(1728): OFI get address vector map failed

Abort(1091215) on node 0 (rank 0 in comm 0): Fatal error in PMPI_Init_thread: Other MPI error, error stack:

MPIR_Init_thread(138)........: 

MPID_Init(1139)..............: 

MPIDI_OFI_mpi_init_hook(1728): OFI get address vector map failed

C/C++ example src/vec/vec/tests/ex47 run successfully with hdf5

Fortran example src/snes/tutorials/ex5f run successfully with 1 MPI process

Completed test examples

Note that the test that fails is the one that uses more than 1 CPU. If I then clone and compile PFLOTRAN, I can only run models using 1 process. If I try to run them using more than one process, PFLOTRAN crashes. I am not sure what the problem is. I tried searching the error on the Internet, but I have not found anything useful.

Thanks,

Jordi

[Hammond, Glenn E]

Jordi,

 

I recommend sending error message below to petsc...@mcs.anl.gov.

 

Glenn

 

From: pflotr...@googlegroups.com <pflotr...@googlegroups.com> On Behalf Of Jordi Sanglas Molist
Sent: Wednesday, June 30, 2021 3:47 AM
To: pflotran-dev <pflotr...@googlegroups.com>
Subject: [pflotran-dev: 6072] Intel installation issue

 

Check twice before you click! This email originated from outside PNNL.

 

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