[firedrake] Problem with installing FireDrake on cluster
Matthew Knepley
knepley at gmail.com
Wed Mar 10 21:06:13 GMT 2021
On Wed, Mar 10, 2021 at 3:48 PM Matthew Knepley <knepley at gmail.com> wrote:
> On Wed, Mar 10, 2021 at 3:15 PM Cynthia Cornelius <cdc at buffalo.edu> wrote:
>
>> Dear Matt,
>>
>> Attached is the log file. Thank you.
>>
>
> Firedrake people, I see a few things:
>
> 1) The PETSc problem is a PTScotch problem. Barry fixed this, but I do not
> know how to specify the PETSc version.
>
> 2) MPICH is being installed, but it should actually point to the cluster
> MPICH
>
> 3) It seems like we should just install PETSc on the cluster with the
> right packages. How should that work with installation?
>
> Cynthia, I will send you a PETSc configure that is like the one I already
> have, but with the Firedrake packages. We will build
> it from the most recent snapshot to avoid the PTScotch problem.
>
Get the source
git clone https://gitlab.com/petsc/petsc.git
which should be the 'main' branch. I have these modules
[knepley at vortex2:~]$ module list
Currently Loaded Modules:
1) intel/17.0 2) intel-mpi/2017.0.1 3) mkl/2017.0.1 4) cmake/3.17.1
I think they need Eigen (ugh), so we do
wget https://gitlab.com/libeigen/eigen/-/archive/3.3.3/eigen-3.3.3.tar.bz2
.
Then you configure is the root
cd petsc
./configure
--prefix=/path/to/installation \
--PETSC_ARCH=default \
--COPTFLAGS='-g -O3 -xCORE-AVX512 -fp-model fast=2' \
--CXXOPTFLAGS='-g -O3 -xCORE-AVX512 -fp-model fast=2' \
--download-chaco \
--download-ctetgen \
--download-eigen=../eigen-3.3.3.tgz \
--download-hdf5 \
--download-hwloc \
--download-hypre \
--download-metis \
--download-ml \
--download-mumps \
--download-netcdf \
--download-parmetis \
--download-pastix \
--download-pnetcdf \
--download-ptscotch \
--download-scalapack \
--download-suitesparse \
--download-superlu_dist \
--download-triangle \
--with-blaslapack-dir=/util/academic/intel/17.0/compilers_and_libraries/linux/mkl
\
--with-c2html=0 \
--with-cxx-dialect=C++11 \
--with-debugging=0 \
--with-fortran-bindings=0 \
--with-shared-libraries=1 \
--with-zlib
Hopefully that works.
Thanks,
Matt
Thanks,
>
> Matt
>
>
>
>> Best regards,
>> Cynthia
>>
>> Cynthia Cornelius
>> HPC Systems Analyst
>> Center for Computational Research
>> University at Buffalo
>> ------------------------------
>> *From:* Matthew Knepley <knepley at gmail.com>
>> *Sent:* Wednesday, March 10, 2021 2:53 PM
>> *To:* Cynthia Cornelius <cdc at buffalo.edu>
>> *Cc:* firedrake at imperial.ac.uk <firedrake at imperial.ac.uk>
>> *Subject:* Re: [firedrake] Problem with installing FireDrake on cluster
>>
>> 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
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>>
>>
>>
>> --
>> 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/>
>>
>
>
> --
> 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/>
>
--
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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