[firedrake] Problem with installing FireDrake on cluster

[Matthew Knepley]

On Wed, Mar 10, 2021 at 2:44 PM Cynthia Cornelius <cdc at buffalo.edu> wrote:

> Greetings,
>
>   I'm trying to install Firedrake software on our cluster.  I cannot use
> sudo nor apt-get.  We have several users who would love to run this
> software on the cluster.  Any suggestions that you may have will be most
> welcome.
>

Hi Cynthia,

Can you send

  /util/academic/firedrake/20210310-basic/firedrake-install.log

  Thanks,

     Matt

Here are the error messages on the screen:
> Depending on your platform, PETSc may take an hour or more to build!
> Traceback (most recent call last):
>   File "firedrake-install", line 1568, in <module>
>     install("petsc/")
>   File "firedrake-install", line 833, in install
>     build_and_install_petsc()
>   File "firedrake-install", line 959, in build_and_install_petsc
>     check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir),
> "PETSC_ARCH={}".format(petsc_arch)] + list(petsc_
> options))
>   File "firedrake-install", line 614, in check_call
>     log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT,
> env=os.environ).decode())
>   File
> "/util/academic/firedrake/20210310-basic/anaconda3/lib/python3.8/subprocess.py",
> line 411, in check_output
>     return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
>   File
> "/util/academic/firedrake/20210310-basic/anaconda3/lib/python3.8/subprocess.py",
> line 512, in run
>     raise CalledProcessError(retcode, process.args,
> subprocess.CalledProcessError: Command
> '['/util/academic/firedrake/20210310-basic/firedrake/bin/python',
> './configure', 'P
> ETSC_DIR=/util/academic/firedrake/20210310-basic/firedrake/src/petsc',
> 'PETSC_ARCH=default', '--with-cxx-dialect=C++11', '
> --download-hwloc', '--with-shared-libraries=1', '--download-mumps',
> '--download-netcdf', '--download-scalapack', '--downlo
> ad-ptscotch', '--download-hypre', '--download-hdf5', '--download-ml',
> '--with-c2html=0', '--download-superlu_dist', '--wit
> h-debugging=0', '--download-pastix', '--download-metis',
> '--download-suitesparse', '--download-pnetcdf', '--with-zlib', '-
> -with-fortran-bindings=0',
> '--download-eigen=/util/academic/firedrake/20210310-basic/firedrake/src/eigen-3.3.3.tgz
> ', '--d
> ownload-chaco', '--download-mpich']' returned non-zero exit status 1.
> Install log saved in
> /util/academic/firedrake/20210310-basic/firedrake-install.log
>
>
> Here are the error messages from the firedrake-install.log:
> make[2]: Leaving directory
> `/util/academic/firedrake/20210310-basic/firedrake/src/petsc/default/externalpackages/git.ptscotc
>
> h/src/libscotch'
> make[1]: Leaving directory
> `/util/academic/firedrake/20210310-basic/firedrake/src/petsc/default/externalpackages/git.ptscotc
> h/src/libscotch'In file included from /usr/include/sys/wait.h:30:0,
>                  from common.h:130,
>                  from common_string.c:57:
> /petsc'
> 2021-03-10 13:37:20,781 DEBUG  New path
> '/util/academic/firedrake/20210310-basic/firedrake/src'
> 2021-03-10 13:37:20,791 INFO
> Install log saved in
> /util/academic/firedrake/20210310-basic/firedrake-install.log
>
> Details of the environment for the build:
> cmake/3.17.1
>
> Anaconda Python 3.8
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ python
> Python 3.8.5 (default, Sep  4 2020, 07:30:14)
> [GCC 7.3.0] :: Anaconda, Inc. on linux
> Type "help", "copyright", "credits" or "license" for more information.
> >>> quit()
>
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ which gcc
> /usr/bin/gcc
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ gcc --version
> gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)
>
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ cat
> /etc/redhat-release
> CentOS Linux release 7.9.2009 (Core)
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ uname -a
> Linux srv-p22-13.cbls.ccr.buffalo.edu 3.10.0-1160.15.2.el7.x86_64 #1 SMP
> Wed Feb 3 15:06:38 UTC 2021 x86_64 x86_64 x86_64 GN
> U/Linux
>
> [cdc at vortex2:/util/academic/firedrake/20210310-basic]$ rpm -qf
> /usr/include/sys/wait.h
> glibc-headers-2.17-323.el7_9.x86_64
>
> Best regards,
>   Cynthia
>
> Cynthia Cornelius
> HPC Systems Analyst
> Center for Computational Research
> University at Buffalo
> _______________________________________________
> firedrake mailing list
> firedrake at imperial.ac.uk
> https://mailman.ic.ac.uk/mailman/listinfo/firedrake
>


-- 
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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