[petsc-dev] Fwd: [petsc-maint] Can't install latest version using spack, complains about superludist cxx clash

Thu Dec 20 14:37:49 CST 2018

This thread is instructive for people who think Spack is a good system.

   Matt

---------- Forwarded message ---------
From: Balay, Satish via petsc-maint <petsc-maint at mcs.anl.gov>
Date: Thu, Dec 20, 2018 at 3:01 PM
Subject: Re: [petsc-maint] Can't install latest version using spack,
complains about superludist cxx clash
To: Syed, Sajid Ali <sajidsyed2021 at u.northwestern.edu>
Cc: Balay, Satish <balay at mcs.anl.gov>, petsc-maint <petsc-maint at mcs.anl.gov>

Can you send the relavent config files?

Try installing with

spack install --keep-stage petsc [options]

[from the build location] send:
spack-build.env
spack-build.out
configure.log

Satish

On Thu, 20 Dec 2018, Sajid Ali via petsc-maint wrote:

> Looking closely, I don’t understand why petsc was ever linked to libblas
> and liblapack at lib64.
>
> Does this have anything to do with the F77 warning ?
>
> [sajid at xrm lib]$ ldd libpetsc.so.3.10.3
>         linux-vdso.so.1 =>  (0x00007ffc2cdef000)
>         libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6385ee8000)
>         libm.so.6 => /lib64/libm.so.6 (0x00007f6385be6000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x00007f63859e2000)
>         libsuperlu_dist.so.6 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/superlu-dist-6.1.0-gi3hicljihkga7x3ew66q5xdyunmmqc3/lib/libsuperlu_dist
> .so.6 (0x00007f6385724000)
>         libmkl_intel_lp64.so =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/intel-mkl-2019.0.117-wzqlcijwx7odz2x5chembudo5leqpfh2/compilers_and_lib
> raries_2019.0.117/linux/mkl/lib/intel64/libmkl_intel_lp64.so
> (0x00007f6384bf3000)
>         libmkl_sequential.so =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/intel-mkl-2019.0.117-wzqlcijwx7odz2x5chembudo5leqpfh2/compilers_and_lib
> raries_2019.0.117/linux/mkl/lib/intel64/libmkl_sequential.so
> (0x00007f638365a000)
>         libmkl_core.so =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/intel-mkl-2019.0.117-wzqlcijwx7odz2x5chembudo5leqpfh2/compilers_and_libraries
> _2019.0.117/linux/mkl/lib/intel64/libmkl_core.so (0x00007f637f521000)
>         libhdf5hl_fortran.so.100 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/hdf5-1.10.4-ltstvsxvyjue2gxfegi4nvr6c5xg3zww/lib/libhdf5hl_fortran.
> so.100 (0x00007f637f304000)
>         libhdf5_fortran.so.100 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/hdf5-1.10.4-ltstvsxvyjue2gxfegi4nvr6c5xg3zww/lib/libhdf5_fortran.so.1
> 00 (0x00007f637f0bc000)
>         libhdf5_hl.so.100 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/hdf5-1.10.4-ltstvsxvyjue2gxfegi4nvr6c5xg3zww/lib/libhdf5_hl.so.100
> (0x0000
> 7f637ee97000)
>         libhdf5.so.103 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/hdf5-1.10.4-ltstvsxvyjue2gxfegi4nvr6c5xg3zww/lib/libhdf5.so.103
> (0x00007f637e
> 8a4000)
>         libparmetis.so =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/parmetis-4.0.3-hw3j2ss7mjsc5x5f2gaflirnuufzptil/lib/libparmetis.so
> (0x00007f6
> 37e66c000)
>         libmetis.so =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/metis-5.1.0-nhgzn4kjskctzmzv35mstvd34nj2ugek/lib/libmetis.so
> (0x00007f637e3fc000
> )
>         libz.so.1 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/zlib-1.2.11-ldu43taplg2nbkxtem346zq4ibhad64i/lib/libz.so.1
> (0x00007f637e1e5000)
>         libX11.so.6 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/libx11-1.6.5-fq4iuwdxjyckf5eqsvnistset6p4hrzm/lib/libX11.so.6
> (0x00007f637deaa00
> 0)
>         libstdc++.so.6 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/gcc-7.3.0-qrjpi76aeo4bysagruwwfii6oneh56lj/lib64/libstdc++.so.6
> (0x00007f637d
> b28000)
>         libmpifort.so.12 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/mpich-3.3-z5uiwmx24jylnivuhlnqjjmm674ozj6x/lib/libmpifort.so.12
> (0x00007f63
> 7d8ef000)
>         libmpi.so.12 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/mpich-3.3-z5uiwmx24jylnivuhlnqjjmm674ozj6x/lib/libmpi.so.12
> (0x00007f637d39c000
> )
>         libgfortran.so.4 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/gcc-7.3.0-qrjpi76aeo4bysagruwwfii6oneh56lj/lib64/libgfortran.so.4
> (0x00007f
> 637cfc9000)
>         libgcc_s.so.1 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/gcc-7.3.0-qrjpi76aeo4bysagruwwfii6oneh56lj/lib64/libgcc_s.so.1
> (0x00007f637cdb
> 1000)
>         libquadmath.so.0 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/gcc-7.3.0-qrjpi76aeo4bysagruwwfii6oneh56lj/lib64/libquadmath.so.0
> (0x00007f
> 637cb72000)
>         libc.so.6 => /lib64/libc.so.6 (0x00007f637c7af000)
>         /lib64/ld-linux-x86-64.so.2 (0x0000562660743000)
>         liblapack.so.3 => /lib64/liblapack.so.3 (0x00007f637c051000)
>         libblas.so.3 => /lib64/libblas.so.3 (0x00007f637bdf7000)
>         libmpicxx.so.12 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/mpich-3.3-z5uiwmx24jylnivuhlnqjjmm674ozj6x/lib/libmpicxx.so.12
> (0x00007f637b
> bd6000)
>         libgomp.so.1 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/gcc-7.3.0-qrjpi76aeo4bysagruwwfii6oneh56lj/lib64/libgomp.so.1
> (0x00007f637b9a80
> 00)
>         libxcb.so.1 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/libxcb-1.13-w3g6d3ulogwz3cxf5brw3ymiw22apkax/lib/libxcb.so.1
> (0x00007f637b780000
> )
>         libXau.so.6 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/libxau-1.0.8-kv6fes6sr7z5mu6gkmpanmzx2tmbaroc/lib/libXau.so.6
> (0x00007f637b57c00
> 0)
>         libXdmcp.so.6 =>
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/libxdmcp-1.1.2-pogqqdhqufmv567ch6n4eipdw7wgpdui/lib/libXdmcp.so.6
> (0x00007f637
> b375000)
>         libudev.so.1 => /lib64/libudev.so.1 (0x00007f637b360000)
>         libxml2.so.2 => /lib64/libxml2.so.2 (0x00007f637aff6000)
>         librt.so.1 => /lib64/librt.so.1 (0x00007f637aded000)
>         libgfortran.so.3 => /lib64/libgfortran.so.3
> (0x00007f637aacb000)
>         libcap.so.2 => /lib64/libcap.so.2 (0x00007f637a8c5000)
>         libdw.so.1 => /lib64/libdw.so.1 (0x00007f637a67e000)
>         liblzma.so.5 => /lib64/liblzma.so.5 (0x00007f637a458000)
>         libattr.so.1 => /lib64/libattr.so.1 (0x00007f637a252000)
>         libelf.so.1 => /lib64/libelf.so.1 (0x00007f637a03a000)
>         libbz2.so.1 => /lib64/libbz2.so.1 (0x00007f6379e2a000)
> [sajid at xrm lib]$ pwd
>
/raid/home/sajid/packages/spack/opt/spack/linux-rhel7-x86_64/gcc-7.3.0/petsc-3.10.3-7fyzhapqnl6qkcuidwugoizr6yt4ujil/lib
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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