Configure error on ARCHER
I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps: cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py firedrake.env contains: module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda # Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules # Load build environment module load fdrake-build-env module load fdrake-python-env export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2
On 31/12/14 16:22, Jacobs, Christian T wrote:
I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps:
cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py
firedrake.env contains:
module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda
# Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules
# Load build environment module load fdrake-build-env module load fdrake-python-env
export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc
The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2
I would need configure.log to be able to say anything. Afaik no one has tried configuring with ml on ARCHER, so it may work with our reconfigure script. Happy New Year! Florian
Hi Florian, Happy New Year. It turns out that I was actually using a different script to the one here: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py. When I use the /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py script, the configuration is successful (https://gist.github.com/ctjacobs/508c195437304afdb65e). However, "make PETSC_DIR=/work/n01/n01/ctjacobs//build_new/petsc PETSC_ARCH=cray-gnu-shared all" then fails with a "No rule to make target" error: https://gist.github.com/ctjacobs/dbcbcb07d6f48b837ad0 . Any ideas? Note that this is using an up-to-date download of https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2, and not a clone of https://bitbucket.org/petsc/petsc.git. Cheers, Christian ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Florian Rathgeber [florian.rathgeber@imperial.ac.uk] Sent: 01 January 2015 09:31 To: firedrake Subject: Re: [firedrake] Configure error on ARCHER On 31/12/14 16:22, Jacobs, Christian T wrote:
I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps:
cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py
firedrake.env contains:
module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda
# Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules
# Load build environment module load fdrake-build-env module load fdrake-python-env
export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc
The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2
I would need configure.log to be able to say anything. Afaik no one has tried configuring with ml on ARCHER, so it may work with our reconfigure script. Happy New Year! Florian
On 02/01/15 11:16, Jacobs, Christian T wrote:
Hi Florian,
Happy New Year.
It turns out that I was actually using a different script to the one here: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py. When I use the /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py script, the configuration is successful (https://gist.github.com/ctjacobs/508c195437304afdb65e). However, "make PETSC_DIR=/work/n01/n01/ctjacobs//build_new/petsc PETSC_ARCH=cray-gnu-shared all" then fails with a "No rule to make target" error: https://gist.github.com/ctjacobs/dbcbcb07d6f48b837ad0 . Any ideas? Note that this is using an up-to-date download of https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2, and not a clone of https://bitbucket.org/petsc/petsc.git.
Yes, reconfigure-cray-gnu-shared.py is the one to use. For that failure I'd need to see make.log. I've also given it another go and had to go down to 12 build threads (have updated the reconfigure script). PETSc builds, but petsc4py does not, it seems the DMPlexDistribute signature has changed: src/petsc4py.PETSc.c:202625:47: error: too many arguments to function 'DMPlexDistribute' __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistribute(__pyx_v_self->__pyx_base.dm, __pyx_v_cpart, __pyx_v_coverlap, (&__pyx_v_pointsf->sf), (&__pyx_v _pardm))); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[40]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/y07/y07/fdrake/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:343, from src/PETSc.c:3: /work/y07/y07/fdrake/petsc/include/petscdmplex.h:185:29: note: declared here PETSC_EXTERN PetscErrorCode DMPlexDistribute(DM, PetscInt, PetscSF*, DM*); Michael, Lawrence, ideas? Florian
Cheers, Christian ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Florian Rathgeber [florian.rathgeber@imperial.ac.uk] Sent: 01 January 2015 09:31 To: firedrake Subject: Re: [firedrake] Configure error on ARCHER
On 31/12/14 16:22, Jacobs, Christian T wrote:
I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps:
cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py
firedrake.env contains:
module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda
# Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules
# Load build environment module load fdrake-build-env module load fdrake-python-env
export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc
The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2
I would need configure.log to be able to say anything. Afaik no one has tried configuring with ml on ARCHER, so it may work with our reconfigure script.
Happy New Year!
Florian
On 02/01/15 12:08, Florian Rathgeber wrote:
On 02/01/15 11:16, Jacobs, Christian T wrote:
Hi Florian,
Happy New Year.
It turns out that I was actually using a different script to the one here: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py. When I use the /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py script, the configuration is successful (https://gist.github.com/ctjacobs/508c195437304afdb65e). However, "make PETSC_DIR=/work/n01/n01/ctjacobs//build_new/petsc PETSC_ARCH=cray-gnu-shared all" then fails with a "No rule to make target" error: https://gist.github.com/ctjacobs/dbcbcb07d6f48b837ad0 . Any ideas? Note that this is using an up-to-date download of https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2, and not a clone of https://bitbucket.org/petsc/petsc.git.
Yes, reconfigure-cray-gnu-shared.py is the one to use. For that failure I'd need to see make.log.
I've also given it another go and had to go down to 12 build threads (have updated the reconfigure script). PETSc builds, but petsc4py does not, it seems the DMPlexDistribute signature has changed:
src/petsc4py.PETSc.c:202625:47: error: too many arguments to function 'DMPlexDistribute' __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistribute(__pyx_v_self->__pyx_base.dm, __pyx_v_cpart, __pyx_v_coverlap, (&__pyx_v_pointsf->sf), (&__pyx_v _pardm))); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[40]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/y07/y07/fdrake/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:343, from src/PETSc.c:3: /work/y07/y07/fdrake/petsc/include/petscdmplex.h:185:29: note: declared here PETSC_EXTERN PetscErrorCode DMPlexDistribute(DM, PetscInt, PetscSF*, DM*);
Michael, Lawrence, ideas?
Ignore that! I was on the wrong branch (master rather than firedrake). Christian, I built successfully with /work/y07/y07/fdrake/build_petsc.sh
Florian
Cheers, Christian ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Florian Rathgeber [florian.rathgeber@imperial.ac.uk] Sent: 01 January 2015 09:31 To: firedrake Subject: Re: [firedrake] Configure error on ARCHER
On 31/12/14 16:22, Jacobs, Christian T wrote:
I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps:
cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py
firedrake.env contains:
module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda
# Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules
# Load build environment module load fdrake-build-env module load fdrake-python-env
export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc
The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2
I would need configure.log to be able to say anything. Afaik no one has tried configuring with ml on ARCHER, so it may work with our reconfigure script.
Happy New Year!
Florian
Thanks Florian. I've got a working build now. Cheers, Christian ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Florian Rathgeber [florian.rathgeber@imperial.ac.uk] Sent: 02 January 2015 14:46 To: firedrake Subject: Re: [firedrake] Configure error on ARCHER On 02/01/15 12:08, Florian Rathgeber wrote:
On 02/01/15 11:16, Jacobs, Christian T wrote:
Hi Florian,
Happy New Year.
It turns out that I was actually using a different script to the one here: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py. When I use the /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py script, the configuration is successful (https://gist.github.com/ctjacobs/508c195437304afdb65e). However, "make PETSC_DIR=/work/n01/n01/ctjacobs//build_new/petsc PETSC_ARCH=cray-gnu-shared all" then fails with a "No rule to make target" error: https://gist.github.com/ctjacobs/dbcbcb07d6f48b837ad0 . Any ideas? Note that this is using an up-to-date download of https://bitbucket.org/mapdes/petsc/get/firedrake.tar.bz2, and not a clone of https://bitbucket.org/petsc/petsc.git.
Yes, reconfigure-cray-gnu-shared.py is the one to use. For that failure I'd need to see make.log.
I've also given it another go and had to go down to 12 build threads (have updated the reconfigure script). PETSc builds, but petsc4py does not, it seems the DMPlexDistribute signature has changed:
src/petsc4py.PETSc.c:202625:47: error: too many arguments to function 'DMPlexDistribute' __pyx_t_4 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistribute(__pyx_v_self->__pyx_base.dm, __pyx_v_cpart, __pyx_v_coverlap, (&__pyx_v_pointsf->sf), (&__pyx_v _pardm))); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[40]; __pyx_lineno = 488; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/y07/y07/fdrake/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:343, from src/PETSc.c:3: /work/y07/y07/fdrake/petsc/include/petscdmplex.h:185:29: note: declared here PETSC_EXTERN PetscErrorCode DMPlexDistribute(DM, PetscInt, PetscSF*, DM*);
Michael, Lawrence, ideas?
Ignore that! I was on the wrong branch (master rather than firedrake). Christian, I built successfully with /work/y07/y07/fdrake/build_petsc.sh
Florian
Cheers, Christian ________________________________________ From: firedrake-bounces@imperial.ac.uk [firedrake-bounces@imperial.ac.uk] on behalf of Florian Rathgeber [florian.rathgeber@imperial.ac.uk] Sent: 01 January 2015 09:31 To: firedrake Subject: Re: [firedrake] Configure error on ARCHER
On 31/12/14 16:22, Jacobs, Christian T wrote:
I'm trying to build an up-to-date version of PETSc on ARCHER. I'm using the script in the Firedrake petsc directory for configuring: /work/y07/y07/fdrake/petsc/reconfigure-cray-gnu-shared.py and the following steps:
cd $WORK/build_new/petsc source ~/firedrake.env python reconfigure-cray-gnu-shared.py
firedrake.env contains:
module unload PrgEnv-cray module load PrgEnv-gnu module unload python module load anaconda
# Add fdrake module path export FDRAKE_DIR=/work/y07/y07/fdrake module use $FDRAKE_DIR/modules
# Load build environment module load fdrake-build-env module load fdrake-python-env
export PETSC_ARCH=cray-gnu-shared export PETSC_DIR=$WORK/build_new/petsc
The configuration step fails with a segmentation fault when making 'ml'. Has anyone else encountered this issue? Does the configuration script need updating? output_configure.log: https://gist.github.com/ctjacobs/8611d07eae5dfb1f39f2
I would need configure.log to be able to say anything. Afaik no one has tried configuring with ml on ARCHER, so it may work with our reconfigure script.
Happy New Year!
Florian
participants (2)
-
Florian Rathgeber
-
Jacobs, Christian T