Actually, looking through the log file, I see PETSc which says to run
make install, but easybuild runs "make" without the install option:
3693 make[2]: Leaving directory
'/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/petsc-3.7.5'
3694 =========================================
3695 make[1]: Leaving directory
'/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/petsc-3.7.5'
3696 Now to install the libraries do:
3697 make
PETSC_DIR=/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/petsc-3.7.5/
PETSC_ARCH=arch-linux2-c-opt install
3698 =========================================
3699
3700 == 2017-02-22 15:08:25,451 run.py:443 INFO cmd " make
PETSC_DIR=/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/petsc-3.7.5/ "
exited with exitcode 0 and output:
3701 make[1]: Entering directory
'/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/petsc-3.7.5'
It runs "make install" later, but not with the arguments that PETSc
instructs to use:
[mboisson@build-node easybuild-framework]$ grep "run.py:443 INFO cmd"
/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/easybuild/easybuild-PETSc-3.7.5-20170222.150836.log
== 2017-02-22 15:07:35,710 run.py:443 INFO cmd " ./configure
--prefix=/home/mboisson/easybuild/software/2017/avx2/MPI/intel2016.4/openmpi2.0/petsc/3.7.5
--with-fftw=1 --with-fftw-dir=$EBROOTFFTW --with-mkl_pardiso=1
--with-mkl_pardiso-dir=$MKLROOT --with-shared-libraries=1
--download-mumps=yes --download-ptscotch=yes --download-superlu=yes
--download-superlu_dist=yes --download-parmetis=yes --download-metis=yes
--download-ml=yes --download-suitesparse=yes --download-hypre=yes
--with-cc="mpicc" --with-cxx="mpicxx" --with-c++-support
--with-fc="mpifort" --CFLAGS="-O2 -xCore-AVX2 -ftz -fp-speculation=safe
-fp-model source -fPIC" --CXXFLAGS="-O2 -xCore-AVX2 -ftz
-fp-speculation=safe -fp-model source -fPIC" --FFLAGS="-O2 -xCore-AVX2
-ftz -fp-speculation=safe -fp-model source -fPIC"
--with-gnu-compilers=0 --with-mpi=1 --with-build-step-np=8
--with-shared-libraries=1 --with-debugging=0 --with-pic=1 --with-x=0
--with-windows-graphics=0 --with-scalapack=1
--with-scalapack-include=$MKLROOT/include
--with-scalapack-lib=[$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a,libmkl_blacs_openmpi_lp64.a,libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a]
--with-blas-lapack-lib=[$MKLROOT/lib/intel64/libmkl_intel_lp64.a,libmkl_sequential.a,libmkl_core.a]
--with-imkl=1
--with-imkl-dir=/cvmfs/soft.computecanada.ca/easybuild/software/2017/Core/imkl/11.3.4.258
" exited with exitcode 0 and output:
== 2017-02-22 15:08:25,451 run.py:443 INFO cmd " make
PETSC_DIR=/dev/shm/mboisson/PETSc/3.7.5/iompi-2016.4/petsc-3.7.5/ "
exited with exitcode 0 and output:
== 2017-02-22 15:08:34,357 run.py:443 INFO cmd "make test" exited with
exitcode 0 and output:
== 2017-02-22 15:08:34,762 run.py:443 INFO cmd " make install " exited
with exitcode 0 and output:
On 17-02-22 11:17, Maxime Boissonneault wrote:
Hi Alan,
I don't think so. Looking at the source code of petsc.py, that skips
the "make install".
That would be if I wanted to compiled in the source directory and
expected it to remain there.
In the past, I have never done this except for OpenFOAM. Typically,
the "make install" of PETSc will copy the external packages as well as
PETSc itself, but in this case, it is not for some reason.
Maxime
On 17-02-22 11:12, Alan O'Cais wrote:
Hi Maxime,
You are probably missing:
sourceinstall = True
in your easyconfig.
Alan
On 22 February 2017 at 17:03, Maxime Boissonneault
<[email protected]
<mailto:[email protected]>> wrote:
Hi Inge,
Thanks. I am trying to do this. However, while PETSc compiles
fine, it seems that it does not install hypre, metis, etc. in the
petsc folder.
When I installed it manually (a different version though), it did
copy those files.
Have you run into this ?
Maxime
On 17-02-22 02:10, Inge Gutheil wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
I remember that at some time there were incompatibilities
between the
at that time current versions of two packages that PETSc both
could
use and that at that time you had to use the versions that
PETSc tried
to download.
In the beginning I also tried to install the packages that I
wanted to
be used by PETSc seperately (it was before I even had heard of
easybuild, and on BlueGene/Q we still do not use easybuild) and I
always had troubles with compatibility. Thus I decided to
only use
download ... except for the MKL things. I only install the static
version of PETSc, thus no problem with LD_LIBRARY_PATH
finding the
wrong packages. The only poblem I have is with our easybuild
head, he
thinks that it is bad to have so many versions installed,
with and
witout debug, with and without 8-Byte integer and with and
without
complex numbers as default. I use the petsc easyblock and
just add the
- --download... options as configopts for example
'--with-large-file-io --download-hypre=1 --download-metis=1
- --download-parmetis=1 --download-spooles=1 --download-superlu=1
- --download-superlu_dist=1 --download-mumps=1 --download-spai=1
- --download-chaco=1 --download-sundials=1 --download-triangle=1
- --download-parms=1 --download-hdf5=1'
and that works.
Inge
On 02/22/17 07:53, Åke Sandgren wrote:
On 02/22/2017 03:40 AM, Maxime Boissonneault wrote:
Thanks Robert, While I understand and am all in favor
of reusing
dependencies, most packages with dependencies do not
provide
download hooks for specific versions of their
dependencies. PETSc
is this way, I believe OpenFoam too. When the
developers go
through this trouble, I prefer to assume that they
know what they
are doing and test with specific versions of
Unfortunately they rarely do (when it comes to HPC
systems and
performance issues at least), they just know that the
ordinary
user knows even less and try to make it easy for them.
the dependencies. If a user finds a bug, it will be
that much
simpler to diagnose if it uses the same versions as the
developers.
The main reason i see for NOT letting codes like PETSc do
their
own download and build of sub dependencies, is that those
dependencies will not be built in the best way, i.e.,
they will be
suboptimal in speed and sometimes even buggy.
But it is always a question of how much time do you have
to keep
things in sync and updated...
I usually prefer to build and test myself and then force
PETSc
et.al <http://et.al>. to use what i already have. But
lately the rate of incoming
software requests for new stuff has been climbing through
the roof.
The curse of having a brand new system with lots of toys...
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------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR
B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt
(Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald
Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
--
---------------------------------
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval
Président - Comité de coordination du soutien à la recherche de
Calcul Québec
Team lead - Research Support National Team, Compute Canada
Instructeur Software Carpentry
Ph. D. en physique
--
Dr. Alan O'Cais
E-CAM Software Manager
Juelich Supercomputing Centre
Forschungszentrum Juelich GmbH
52425 Juelich, Germany
Phone: +49 2461 61 5213
Fax: +49 2461 61 6656
E-mail: [email protected] <mailto:[email protected]>
WWW: http://www.fz-juelich.de/ias/jsc/EN
--
---------------------------------
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval
Président - Comité de coordination du soutien à la recherche de Calcul Québec
Team lead - Research Support National Team, Compute Canada
Instructeur Software Carpentry
Ph. D. en physique
--
---------------------------------
Maxime Boissonneault
Analyste de calcul - Calcul Québec, Université Laval
Président - Comité de coordination du soutien à la recherche de Calcul Québec
Team lead - Research Support National Team, Compute Canada
Instructeur Software Carpentry
Ph. D. en physique
