[petsc-users] PETSc on fedora 36

Tue Aug 23 10:33:58 CDT 2022

Hm - I don't see this.

[root at pj01 ~]# ldd /usr/lib64/libpetsc64.so
	linux-vdso.so.1 => linux-vdso.so.1 (0x00007ffd10f66000)
	libflexiblas64.so.3 => /lib64/libflexiblas64.so.3 (0x00007f9e1fe00000)
	libcgns.so.4.3 => /lib64/libcgns.so.4.3 (0x00007f9e1fd19000)
	libhdf5.so.200 => /lib64/libhdf5.so.200 (0x00007f9e1f800000)
	libmetis64.so.0 => /lib64/libmetis64.so.0 (0x00007f9e219a8000)
	libm.so.6 => /lib64/libm.so.6 (0x00007f9e1fc3b000)
	libX11.so.6 => /lib64/libX11.so.6 (0x00007f9e1f6b9000)
	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f9e1f400000)
	libc.so.6 => /lib64/libc.so.6 (0x00007f9e1f228000)
	libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f9e1ee00000)
	libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f9e2195e000)
	/lib64/ld-linux-x86-64.so.2 => /lib64/ld-linux-x86-64.so.2 (0x00007f9e21a24000)
	libsz.so.2 => /lib64/libsz.so.2 (0x00007f9e21955000)
	libz.so.1 => /lib64/libz.so.1 (0x00007f9e2193b000)
	libpcre2-posix.so.3 => /lib64/libpcre2-posix.so.3 (0x00007f9e21934000)
	libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f9e201b6000)
	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f9e1fc1b000)
	libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f9e1f68e000)
	libpcre2-8.so.0 => /lib64/libpcre2-8.so.0 (0x00007f9e1f18b000)
	libXau.so.6 => /lib64/libXau.so.6 (0x00007f9e1fc15000)

[root at pj01 ~]# rpm -ql petsc64-devel |grep petscconf.h
/usr/include/petsc64/petscconf.h
[root at pj01 ~]# grep MPIUNI /usr/include/petsc64/petscconf.h
#define PETSC_HAVE_MPIUNI 1

So /usr/lib64/libpetsc64.so appears to be a sequential build [for me]

Satish

On Tue, 23 Aug 2022, Rafel Amer Ramon wrote:

> 
> Hi,
> 
> mpicc and mpirun are from the package openmpi-devel-4.1.2-3.fc36.x86_64
> and the petsc64 library is linked with  /usr/lib64/openmpi/lib/libmpi.so.40
> 
> ~# ldd /lib64/libpetsc64.so.3.16.4 
> 	linux-vdso.so.1 (0x00007fff5becc000)
> 	libflexiblas64.so.3 => /lib64/libflexiblas64.so.3 (0x00007f3030e30000)
> 	libcgns.so.4.2 => /usr/lib64/openmpi/lib/libcgns.so.4.2 (0x00007f3030d46000)
> 	libhdf5.so.200 => /usr/lib64/openmpi/lib/libhdf5.so.200 (0x00007f303091a000)
> 	libm.so.6 => /lib64/libm.so.6 (0x00007f303083c000)
> 	libX11.so.6 => /lib64/libX11.so.6 (0x00007f30306f4000)
> 	libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f30304c0000)
> 	libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f303049e000)
> 	libc.so.6 => /lib64/libc.so.6 (0x00007f303029c000)
> 	libgfortran.so.5 => /lib64/libgfortran.so.5 (0x00007f302ffcf000)
> 	libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f302ff87000)
> 	/lib64/ld-linux-x86-64.so.2 (0x00007f30327bb000)
> 	libmpi.so.40 => /usr/lib64/openmpi/lib/libmpi.so.40 (0x00007f302fe59000)
> 	libsz.so.2 => /lib64/libsz.so.2 (0x00007f302fe50000)
> 	libz.so.1 => /lib64/libz.so.1 (0x00007f302fe34000)
> 	libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f302fe08000)
> 	libopen-rte.so.40 => /usr/lib64/openmpi/lib/libopen-rte.so.40 (0x00007f302fd4d000)
> 	libopen-pal.so.40 => /usr/lib64/openmpi/lib/libopen-pal.so.40 (0x00007f302fc9f000)
> 	libhwloc.so.15 => /lib64/libhwloc.so.15 (0x00007f302fc42000)
> 	libevent_core-2.1.so.7 => /lib64/libevent_core-2.1.so.7 (0x00007f302fc07000)
> 	libevent_pthreads-2.1.so.7 => /lib64/libevent_pthreads-2.1.so.7 (0x00007f302fc02000)
> 	libXau.so.6 => /lib64/libXau.so.6 (0x00007f302fbfc000)
> 
> I think that it's correct, but it don't work.
> 
> Best regards,
> 
> Rafel Amer
> 
> El 22/8/22 a les 20:36, Barry Smith ha escrit:
> 
>   Are you sure the mpirun you are using matches the mpi that PETSc was built with? 
> 
>       On Aug 22, 2022, at 2:31 PM, Rafel Amer Ramon <rafel.amer at upc.edu> wrote:
> 
> Hi,
> 
> I have installed the following packages on fedora 36
> 
> ~# rpm -qa | grep petsc
> petsc64-3.16.4-3.fc36.x86_64
> petsc-3.16.4-3.fc36.x86_64
> petsc-openmpi-3.16.4-3.fc36.x86_64
> petsc-openmpi-devel-3.16.4-3.fc36.x86_64
> python3-petsc-openmpi-3.16.4-3.fc36.x86_64
> petsc-devel-3.16.4-3.fc36.x86_64
> petsc64-devel-3.16.4-3.fc36.x86_64
> 
> ~# rpm -qa | grep openmpi
> openmpi-4.1.2-3.fc36.x86_64
> ptscotch-openmpi-6.1.2-2.fc36.x86_64
> scalapack-openmpi-2.1.0-11.fc36.x86_64
> openmpi-devel-4.1.2-3.fc36.x86_64
> MUMPS-openmpi-5.4.1-2.fc36.x86_64
> superlu_dist-openmpi-6.1.1-9.fc36.x86_64
> hdf5-openmpi-1.12.1-5.fc36.x86_64
> hypre-openmpi-2.18.2-6.fc36.x86_64
> petsc-openmpi-3.16.4-3.fc36.x86_64
> fftw-openmpi-libs-double-3.3.10-2.fc36.x86_64
> fftw-openmpi-libs-long-3.3.10-2.fc36.x86_64
> fftw-openmpi-libs-single-3.3.10-2.fc36.x86_64
> fftw-openmpi-libs-3.3.10-2.fc36.x86_64
> fftw-openmpi-devel-3.3.10-2.fc36.x86_64
> petsc-openmpi-devel-3.16.4-3.fc36.x86_64
> python3-petsc-openmpi-3.16.4-3.fc36.x86_64
> scalapack-openmpi-devel-2.1.0-11.fc36.x86_64
> python3-openmpi-4.1.2-3.fc36.x86_64
> hdf5-openmpi-devel-1.12.1-5.fc36.x86_64
> cgnslib-openmpi-4.2.0-6.fc36.x86_64
> cgnslib-openmpi-devel-4.2.0-6.fc36.x86_64
> 
> and I try to compile and run the program written in the file e.c
> 
> ~# cat e.c
> #include <petsc.h>
> 
> int main(int argc, char **argv) {
>   PetscErrorCode ierr;
>   PetscMPIInt    rank;
> 
>   ierr = PetscInitialize(&argc,&argv,NULL,
>       "Compute e in parallel with PETSc.\n\n"); if (ierr) return ierr;
>   ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank); CHKERRQ(ierr);
>   ierr = PetscPrintf(PETSC_COMM_WORLD,"My rank is %d\n",rank); CHKERRQ(ierr);
> 
>   
>   return PetscFinalize();
> }
> 
> I compile it with the command
> 
> ~# mpicc -o e e.c -I/usr/include/petsc64 -lpetsc64
> 
> and I run it with
> 
> ~# mpirun -np 8 ./e
> My rank is 0
> My rank is 0
> My rank is 0
> My rank is 0
> My rank is 0
> My rank is 0
> My rank is 0
> My rank is 0
> 
> but all my process get rank 0.
> 
> Do you know what I'm doing wrong?
> 
> Thank you!!
> 
> Best regards,
> 
> Rafel Amer
> 
> 
> 
> 
> 