[petsc-users] libpciaccess dependency Problem

[Jed Brown]

Make sure your batch environment has the same modules loaded so you get
the same versions of all the libraries.

Aroli Marcellinus <aroli.marcellinus at gmail.com> writes:

> When I try to compile the program with PETSC, and run it with mpirun using
> qsub. And I have checked the log and it something like this:
>
> cep2017_heart: error while loading shared libraries: libpciaccess.so.0:
> cannot open shared object file: No such file or directory
>
> and I check ldd, the result is like this:
> ldd bin/cep2017_heart
>     linux-vdso.so.1 =>  (0x00007fff99787000)
>     libsundials_cvode.so.2 =>
> /opt/Lib/sundials-2.7.0/lib/libsundials_cvode.so.2 (0x00002ac2b2262000)
>     libsundials_nvecserial.so.2 =>
> /opt/Lib/sundials-2.7.0/lib/libsundials_nvecserial.so.2 (0x00002ac2b248d000)
>     libsundials_nvecparallel.so.2 =>
> /opt/Lib/sundials-2.7.0/lib/libsundials_nvecparallel.so.2
> (0x00002ac2b2692000)
>     libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000039f0c00000)
>     libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00002ac2b28c7000)
>     libdl.so.2 => /lib64/libdl.so.2 (0x00000039efc00000)
>     libmpi_usempif08.so.20 =>
> /opt/Lib/openmpi-2.1.3/lib/libmpi_usempif08.so.20 (0x00002ac2b2c6a000)
>     libmpi_usempi_ignore_tkr.so.20 =>
> /opt/Lib/openmpi-2.1.3/lib/libmpi_usempi_ignore_tkr.so.20
> (0x00002ac2b2e9d000)
>     libmpi_mpifh.so.20 => /opt/Lib/openmpi-2.1.3/lib/libmpi_mpifh.so.20
> (0x00002ac2b30a6000)
>     libmpi.so.20 => /opt/Lib/openmpi-2.1.3/lib/libmpi.so.20
> (0x00002ac2b3302000)
>     libifport.so.5 =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifport.so.5
> (0x00002ac2b35f5000)
>     libifcore.so.5 =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcore.so.5
> (0x00002ac2b372a000)
>     libimf.so =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libimf.so
> (0x00002ac2b396d000)
>     libsvml.so =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libsvml.so
> (0x00002ac2b3d39000)
>     libm.so.6 => /lib64/libm.so.6 (0x00000039f0000000)
>     libirc.so =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libirc.so
> (0x00002ac2b44ac000)
>     libpthread.so.0 => /lib64/libpthread.so.0 (0x00000039f0400000)
>     libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000035b0800000)
>     libz.so.1 => /lib64/libz.so.1 (0x00000037c7600000)
>     libc.so.6 => /lib64/libc.so.6 (0x00000039ef800000)
>     libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000039f0800000)
>     libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000039f1000000)
>     /lib64/ld-linux-x86-64.so.2 (0x00000039ef000000)
>     libopen-rte.so.20 => /opt/Lib/openmpi-2.1.3/lib/libopen-rte.so.20
> (0x00002ac2b45fb000)
>     libopen-pal.so.20 => /opt/Lib/openmpi-2.1.3/lib/libopen-pal.so.20
> (0x00002ac2b4884000)
>     libpciaccess.so.0 => /usr/lib64/libpciaccess.so.0 (0x00002ac2b4b86000)
>     librt.so.1 => /lib64/librt.so.1 (0x00000039f3c00000)
>     libutil.so.1 => /lib64/libutil.so.1 (0x00000039fca00000)
>     libintlc.so.5 =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libintlc.so.5
> (0x00002ac2b4d8d000)
>     libifcoremt.so.5 =>
> /opt/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcoremt.so.5
> (0x00002ac2b4eda000)
>
>
> So as you can see that the libpciaccess already coupled to the compiled
> program, but it's still error. So I know that libpciaccess maybe from the
> MPI libs (I'm using OpenMPI), but this kind of error is really bugging me.
>
> Even after I tried to use --disable-hwloc-pci when installing OpenMPI, it
> still got this kind of error,.
>
> What I want to know is:
> - Is it possible to remove the dependenciness of libpciaccess?
> - Or how to configure it so that PETSc or MPI doesn't use libpciaccess?
>
> In my case, I cannot use static because some of those dependencies doesn't
> have static libraries.
>
> I'm using:
> PETSc-3.9.0
> OpenMPI-2.1.3
>
>
>
>
> Aroli Marcellinus
>
> *Kumoh Institute of Technology**Computational Medicine Laboratory*
> 61 Daehak-ro (Sinpyeong-dong), Gumi, Gyeongbuk
> +82 10 9724 3957
> KTalk ID: vondarkness