|
| From: | Konstantinos Poulios |
| Subject: | Re: [EXT] Re: getfem installation |
| Date: | Sat, 4 Dec 2021 10:02:25 +0100 |
Dear Dr. Poulios,
Thank you so much for your prompt response and information. They are very helpful. I cc’ed this email to getfem-users@nongnu.org so that I don’t need to send to your personal email in next one. After reading your reference of the configure command, I started from scratch but still got compiling errors.
I installed metis and mumps in the system from EPEL reporistory.
[root@ ~]# rpm -qa |grep metis
metis-devel-5.1.0-12.el7.x86_64
metis-5.1.0-12.el7.x86_64
[root@ ~]# rpm -qa |grep metis
metis-devel-5.1.0-12.el7.x86_64
metis-5.1.0-12.el7.x86_64
[root@ ~]# rpm -qa |grep MUMPS
MUMPS-srpm-macros-5.3.5-1.el7.noarch
MUMPS-5.3.5-1.el7.x86_64
MUMPS-devel-5.3.5-1.el7.x86_64
MUMPS-common-5.3.5-1.el7.noarch
I used the openmpi/4.1.1, gcc/3.9.0, blas/3.8.0 and zlib/1.2.11 modules for this build. Below is the module list command output.
[ris_hpc_apps@r1drpswdev3 getfem-5.4.1]$ module list
Currently Loaded Modules:
1) openmpi/4.1.1 2) python/3.7.3-anaconda 3) blas/3.8.0 4) zlib/1.2.11 5) gcc/9.3.0
Here is my configuration command running on getfem-5.4.1 directory
./configure CXX="/risapps/rhel7/openmpi/4.1.1/bin/mpic++" CC="/risapps/rhel7/openmpi/4.1.1/bin/mpicc" FC="/risapps/rhel7/openmpi/4.1.1/bin/mpifort" LIBS="-L/risapps/rhel7/gcc/9.3.0/lib64 -L/risapps/rhel7/openmpi/4.1.1/lib -L/risapps/rhel7/blas/3.8.0 -L/risapps/rhel7/zlib/1.2.11/lib -L/usr/lib64 -lmetis -lzmumps -ldmumps -lcmumps -lsmumps -lmumps_common" CXXFLAGES="-I/risapps/rhel7/gcc/9.3.0/include -I/risapps/rhel7/openmpi/4.1.1/include -I/risapps/rhel7/zlib/1.2.11/include -I/usr/include -I/usr/include/MUMPS" CPPFLAGES="-I/risapps/rhel7/gcc/9.3.0/include -I/risapps/rhel7/openmpi/4.1.1/include -I/risapps/rhel7/zlib/1.2.11/include -I/usr/include -I/usr/include/MUMPS" CFLAGS="-I/risapps/rhel7/gcc/9.3.0/include -I/risapps/rhel7/openmpi/4.1.1/include -I/risapps/rhel7/zlib/1.2.11/include -I/usr/include -I/usr/include/MUMPS" PYTHON="/risapps/rhel7/python/3.7.3/bin/python" PYTHON_VERSION=3.7.3 --with-mumps="-L/usr/lib64" --with-mumps-include-dir="-I/usr/include/MUMPS" --with-blas="-L/risapps/rhel7/blas/3.8.0" --prefix=/risapps/rhel7/getfem-mpi/5.4.1 --enable-shared --enable-metis --enable-par-mumps -enable-paralevel=2
The current errors on the make command are the following:
….
libtool: compile: /risapps/rhel7/openmpi/4.1.1/bin/mpic++ -DHAVE_CONFIG_H -I. -I.. -I../src -I../src -I.. -I/usr/local/include -DGETFEM_PARA_LEVEL=2 -DGMM_USES_MPI -DGMM_USES_BLAS -DGMM_U SES_BLAS_INTERFACE -I/usr/include/MUMPS -O3 -std=c++14 -MT dal_bit_vector.lo -MD -MP -MF .deps/dal_bit_vector.Tpo -c dal_bit_vector.cc -fPIC -DPIC -o .libs/dal_bit_vector.o
In file included from ./gmm/gmm_kernel.h:49,
from getfem/bgeot_config.h:50,
from getfem/getfem_omp.h:46,
from getfem/dal_basic.h:42,
from getfem/dal_bit_vector.h:51,
from dal_bit_vector.cc:23:
./gmm/gmm_matrix.h:956:32: error: ‘MPI_Datatype’ does not name a type
956 | template <typename T> inline MPI_Datatype mpi_type(T)
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:958:10: error: ‘MPI_Datatype’ does not name a type
958 | inline MPI_Datatype mpi_type(double) { return MPI_DOUBLE; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:959:10: error: ‘MPI_Datatype’ does not name a type
959 | inline MPI_Datatype mpi_type(float) { return MPI_FLOAT; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:960:10: error: ‘MPI_Datatype’ does not name a type
960 | inline MPI_Datatype mpi_type(long double) { return MPI_LONG_DOUBLE; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:962:10: error: ‘MPI_Datatype’ does not name a type
962 | inline MPI_Datatype mpi_type(std::complex<float>) { return MPI_COMPLEX; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:963:10: error: ‘MPI_Datatype’ does not name a type
963 | inline MPI_Datatype mpi_type(std::complex<double>) { return MPI_DOUBLE_COMPLEX; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:965:10: error: ‘MPI_Datatype’ does not name a type
965 | inline MPI_Datatype mpi_type(int) { return MPI_INT; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:966:10: error: ‘MPI_Datatype’ does not name a type
966 | inline MPI_Datatype mpi_type(unsigned int) { return MPI_UNSIGNED; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:967:10: error: ‘MPI_Datatype’ does not name a type
967 | inline MPI_Datatype mpi_type(long) { return MPI_LONG; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h:968:10: error: ‘MPI_Datatype’ does not name a type
968 | inline MPI_Datatype mpi_type(unsigned long) { return MPI_UNSIGNED_LONG; }
| ^~~~~~~~~~~~
./gmm/gmm_matrix.h: In function ‘typename gmm::strongest_value_type3<V1, V2, MATSP>::value_type gmm::vect_sp(const gmm::mpi_distributed_matrix<MAT>&, const V1&, const V2&)’:
./gmm/gmm_matrix.h:1012:50: error: ‘MPI_SUM’ was not declared in this scope
1012 | MPI_Allreduce(&res, &rest, 1, mpi_type(T()), MPI_SUM,MPI_COMM_WORLD);
| ^~~~~~~
./gmm/gmm_matrix.h: In function ‘void gmm::mult_add(const gmm::mpi_distributed_matrix<MAT>&, const V1&, V2&)’:
./gmm/gmm_matrix.h:1023:20: error: there are no arguments to ‘MPI_Wtime’ that depend on a template parameter, so a declaration of ‘MPI_Wtime’ must be available [-fpermissive]
1023 | double t_ref = MPI_Wtime();
| ^~~~~~~~~
./gmm/gmm_matrix.h:1023:20: note: (if you use ‘-fpermissive’, G++ will accept your code, but allowing the use of an undeclared name is deprecated)
./gmm/gmm_matrix.h:1026:21: error: there are no arguments to ‘MPI_Wtime’ that depend on a template parameter, so a declaration of ‘MPI_Wtime’ must be available [-fpermissive]
1026 | double t_ref2 = MPI_Wtime();
| ^~~~~~~~~
./gmm/gmm_matrix.h:1028:19: error: ‘MPI_SUM’ was not declared in this scope
1028 | MPI_SUM,MPI_COMM_WORLD);
| ^~~~~~~
./gmm/gmm_matrix.h:1029:18: error: there are no arguments to ‘MPI_Wtime’ that depend on a template parameter, so a declaration of ‘MPI_Wtime’ must be available [-fpermissive]
1029 | tmult_tot2 = MPI_Wtime()-t_ref2;
| ^~~~~~~~~
./gmm/gmm_matrix.h:1032:17: error: there are no arguments to ‘MPI_Wtime’ that depend on a template parameter, so a declaration of ‘MPI_Wtime’ must be available [-fpermissive]
1032 | tmult_tot = MPI_Wtime()-t_ref;
| ^~~~~~~~~
make[2]: *** [Makefile:941: dal_bit_vector.lo] Error 1
make[2]: Leaving directory '/risapps/build7/getfem-5.4.1/src'
make[1]: *** [Makefile:577: all-recursive] Error 1
make[1]: Leaving directory '/risapps/build7/getfem-5.4.1'
make: *** [Makefile:466: all] Error 2
I really appreciate your help. Thank you again !
Best Regards
Jinzhen Chen
From: Konstantinos Poulios <kopo@mek.dtu.dk>
Date: Tuesday, November 30, 2021 at 1:53 AM
To: "Chen,Jinzhen" <JChen24@mdanderson.org>
Subject: [EXT] Re: getfem installation
WARNING: This email originated from outside of MD Anderson. Please validate the sender's email address before clicking on links or attachments as they may not be safe.
Dear Jinzhen Chen,
Thanks for your question. Yes you should be able to compile GetFEM, also the parallel version of it on Redhat. I haven't tried it but there isn't anything distribution specific in the GetFEM code.
Having said that, the parallel version has not been tested very recently, and it might need some performance fixes from our side, to get a good scaling for Anne Ceciles problem. Having compiled the parallel version of GetFEM on your cluster is a good starting point in any case to detect bottlenecks.
The tricky parts for building GetFEM are normally how to link to mumps, metis and other dependencies. If you could send me the compilation errors that you get, either on this address or on the getfem mailing list getfem-users@nongnu.org I can try to help you to resolve the issues.
As an additional reference, some time ago, when I asked our cluster administrators to compile GetFEM they used the following configure options:
$ ../configure CXX=mpicxx CC=mpicc FC=mpifort LIBS= -L/zdata/groups/common/nicpa/2018-feb/generic/build-tools/1.0/lib -L/zdata/groups/common/nicpa/2018-feb/generic/build-tools/1.0/lib64 -L/zdata/groups/common/nicpa/2018-feb/generic/gcc/7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/generic/gcc/7.3.0/lib64 -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/zlib/1.2.11/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/libxml2/2.9.7/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/hwloc/1.11.9/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/openmpi/3.0.0/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/parmetis/4.0.3/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/scalapack/204/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/openblas/0.2.20/gnu-7.3.0/lib -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/scotch/6.0.4/gnu-7.3.0/lib -L/zdata/g
roups/common/nicpa/2018-feb/XeonX5550/mumps/5.1.2/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/generic/build-tools/1.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/generic/build-tools/1.0/lib64 -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/generic/gcc/7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/generic/gcc/7.3.0/lib64 -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/zlib/1.2.11/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/generic/numactl/2.0.11/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/libxml2/2.9.7/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/hwloc/1.11.9/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/openmpi/3.0.0/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/parmetis/4.0.3/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/scalapack/204/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/Xeon
X5550/openblas/0.2.20/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/scotch/6.0.4/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/mumps/5.1.2/gnu-7.3.0/lib -lzmumps -ldmumps -lcmumps -lsmumps -lmumps_common -lpord -lesmumps -lscotch -lscotcherr -lparmetis -lmetis -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/openblas/0.2.20/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/openblas/0.2.20/gnu-7.3.0/lib -lopenblas --disable-openmp --enable-paralevel --enable-metis --enable-par-mumps --enable-python --disable-boost --disable-matlab --disable-scilab --with-blas= -L/zdata/groups/common/nicpa/2018-feb/XeonX5550/openblas/0.2.20/gnu-7.3.0/lib -Wl,-rpath=/zdata/groups/common/nicpa/2018-feb/XeonX5550/openblas/0.2.20/gnu-7.3.0/lib -lopenblas --prefix=<change-here-for-your-installation-directory>
Best regards
Konstantinos
On Tue, 2021-11-30 at 00:24 +0000, Chen,Jinzhen wrote:
Dear Dr Konstantinos Poulios,
My name is Jinzhen Chen, a HPC administrator on MD Anderson Cancer Center, Houston, USA. I am helping a user (Dr. Lesage,Anne Cecile J) to install getfem on our HPC cluster, which OS is rhel7.9. I got its basic installed. However, When I tried to use option –enable-paralevel=2 of the configure based onhttps://getfem.org/userdoc/parallel.html, I kept getting compiling errors. Looks like some libraries are missing, not visible or not compatible. I have metis and MUMPS installed on the system and used openmpi/4.1.1 module.
My question is it is possible to install the parallel version of getfem on rhel7 ? if so, how can I contact developer or someone for the issues? I really appreciate your help and am looking forward to hearing from you.
Thank you very much !
Regards
Jinzhen Chen – HPC Team
inside:Information Services
inside:HPC Request
Email: jchen24@mdanderson.org | Tel: 713-745-6226
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