[firedrake] Problem with installing FireDrake on cluster
Ham, David A
david.ham at imperial.ac.uk
Wed Mar 10 21:21:15 GMT 2021
You specify the MPI to use by passing the options given here:
https://www.firedrakeproject.org/parallelism.html#installing-for-parallel-use
If you want to use an externally built PETSc then you set PETSC_ARCH and PETSC_DIR, and pass --honour-petsc-dir to firedrake-install. Note British spelling.
You can also run
firedrake-install --show-petsc-configure-options
to print out the options we need you to pass to petsc configure.
Cheers,
David
From: firedrake-bounces at imperial.ac.uk <firedrake-bounces at imperial.ac.uk> on behalf of Matthew Knepley <knepley at gmail.com>
Date: Wednesday, 10 March 2021 at 21:06
To: Cynthia Cornelius <cdc at buffalo.edu>
Cc: firedrake <firedrake at imperial.ac.uk>
Subject: Re: [firedrake] Problem with installing FireDrake on cluster
On Wed, Mar 10, 2021 at 3:48 PM Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:
On Wed, Mar 10, 2021 at 3:15 PM Cynthia Cornelius <cdc at buffalo.edu<mailto: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<mailto:knepley at gmail.com>>
Sent: Wednesday, March 10, 2021 2:53 PM
To: Cynthia Cornelius <cdc at buffalo.edu<mailto:cdc at buffalo.edu>>
Cc: firedrake at imperial.ac.uk<mailto:firedrake at imperial.ac.uk> <firedrake at imperial.ac.uk<mailto: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<mailto: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<http://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
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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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