January 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] openmpi downloaded tarball broken ?
by Jed Brown 03 Jan '21

03 Jan '21

$ sha256sum openmpi-4.1.0.tar.* 73866fb77090819b6a8c85cb8539638d37d6877455825b74e289d647a39fd5b5 openmpi-4.1.0.tar.bz2 228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a openmpi-4.1.0.tar.gz Barry Smith <bsmith(a)petsc.dev> writes: > Any change sites might strip out "dangerous" shell scripts > > I reproduced the same problem several times with different versions of OpenMPI on the UTK xSDK machine. > > >> On Jan 3, 2021, at 9:36 AM, Jed Brown <jed(a)jedbrown.org> wrote: >> >> I don't understand. >> >> $ wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.bz2 >> --2021-01-03 08:35:08-- https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.bz2 >> Resolving download.open-mpi.org (download.open-mpi.org) 143.204.26.61, 143.204.26.76, 143.204.26.58, ... >> Connecting to download.open-mpi.org (download.open-mpi.org)|143.204.26.61|:443... connected. >> HTTP request sent, awaiting response... 200 OK >> Length: 10022171 (9.6M) [binary/octet-stream] >> Saving to: ‘openmpi-4.1.0.tar.bz2’ >> >> openmpi-4.1.0.tar.bz2 100%[==================================>] 9.56M 46.6MB/s in 0.2s >> >> 2021-01-03 08:35:08 (46.6 MB/s) - ‘openmpi-4.1.0.tar.bz2’ saved [10022171/10022171] >> >> $ tar xf openmpi-4.1.0.tar.bz2 >> $ file openmpi-4.1.0/configure >> openmpi-4.1.0/configure: POSIX shell script, ASCII text executable, with very long lines >> >> Barry Smith <bsmith(a)petsc.dev> writes: >> >>> 4.1 is also missing ./configure but documentation clearly states you install openMPI with ./configure ! >>> >>>> On Jan 3, 2021, at 8:31 AM, Barry Smith <bsmith(a)petsc.dev> wrote: >>>> >>>> >>>> $ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> >>>> --2021-01-03 09:24:24-- https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> >>>> Resolving download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)... 13.249.117.107, 13.249.117.91, 13.249.117.41, ... >>>> Connecting to download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)|13.249.117.107|:443... connected. >>>> HTTP request sent, awaiting response... 200 OK >>>> Length: 17418534 (17M) [binary/octet-stream] >>>> Saving to: ‘openmpi-4.0.3.tar.gz’ >>>> >>>> 100%[=======================================================================>] 17,418,534 49.1MB/s in 0.3s >>>> >>>> 2021-01-03 09:24:26 (49.1 MB/s) - ‘openmpi-4.0.3.tar.gz’ saved [17418534/17418534] >>>> >>>> ~ arch-fix-cuda-ccbin-wrong-arguments >>>> $ cd petsc >>>> ~/petsc (barry/2020-12-31/fix-cuda-ccbin-wrong-arguments>) arch-fix-cuda-ccbin-wrong-arguments >>>> $ ./configure --download-openmpi=../openmpi-4.0.3.tar.gz --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-cuda --download-slepc >>>> =============================================================================== >>>> Configuring PETSc to compile on your system >>>> =============================================================================== >>>> ============================================================================================= ***** WARNING: F77 (set to /nfs/apps/spacks/2020-10-22/opt/spack/linux-centos7-x86_64/gcc-7.3.0/gcc-7.3.0-l use ./configure F77=$F77 if you really want to use that value ****** ============================================================================================= ============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports, or use the --download-make option to get the latest GNU make ***** ============================================================================================= ============================================================================================= It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org <http://www.valgrind.org/> Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure ============================================================================================= ============================================================================================= Running libtoolize on OPENMPI; this may take several minutes ============================================================================================= ============================================================================================= Running autoreconf on OPENMPI; this may take several minutes ============================================================================================= ******************************************************************************* >>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >>>> ------------------------------------------------------------------------------- >>>> Error running libtoolize or autoreconf on OPENMPI: Could not execute "[['/usr/bin/autoreconf', '--force', '--install']]": >>>> autoreconf: 'configure.ac' or 'configure.in' is required >>>> ******************************************************************************* >>>> >>>>

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Re: [petsc-dev] false positive test
by Barry Smith 03 Jan '21

03 Jan '21

There is MR to fix this problem. https://gitlab.com/petsc/petsc/-/merge_requests/3531 <https://gitlab.com/petsc/petsc/-/merge_requests/3531> I have added you as a reviewer. Other reviewers have been ignoring this crucial fix. Barry > On Jan 3, 2021, at 10:49 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > > My test will fail if the gold output file is missing but otherwise it seems to always succeed. I just branched this from master. > Any ideas? > > (base) 11:37 adams/landau-cleanup *= ~/Codes/petsc$ rm src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out > remove src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out? y > (base) 11:37 adams/landau-cleanup *= ~/Codes/petsc$ touch /Users/markadams/Codes/petsc/src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out > (base) 11:45 2 adams/landau-cleanup *= ~/Codes/petsc$ make -f gmakefile --debug test search='ts_utils_dmplexlandau_tutorials-ex2_0' > GNU Make 3.81 > Copyright (C) 2006 Free Software Foundation, Inc. > This is free software; see the source for copying conditions. > There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A > PARTICULAR PURPOSE. > > This program built for i386-apple-darwin11.3.0 > Reading makefiles... > Updating goal targets.... > File `test' does not exist. > File `report_tests' does not exist. > File `starttime' does not exist. > File `pre-clean' does not exist. > Must remake target `pre-clean'. > Using MAKEFLAGS: --debug=basic -- search=ts_utils_dmplexlandau_tutorials-ex2_0 > Successfully remade target file `pre-clean'. > Must remake target `starttime'. > Successfully remade target file `starttime'. > File `ts_utils_dmplexlandau_tutorials-ex2_0' does not exist. > File `arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts' does not exist. > Must remake target `arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts'. > TEST arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts > ok ts_utils_dmplexlandau_tutorials-ex2_0 > ok diff-ts_utils_dmplexlandau_tutorials-ex2_0 > Successfully remade target file `arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts'. > Must remake target `ts_utils_dmplexlandau_tutorials-ex2_0'. > Successfully remade target file `ts_utils_dmplexlandau_tutorials-ex2_0'. > Must remake target `report_tests'. > > # ------------- > # Summary > # ------------- > # success 2/2 tests (100.0%) > # failed 0/2 tests (0.0%) > # todo 0/2 tests (0.0%) > # skip 0/2 tests (0.0%) > # > # Wall clock time for tests: 7 sec > # Approximate CPU time (not incl. build time): 6.97 sec > # > # Timing summary (actual test time / total CPU time): > # ts_utils_dmplexlandau_tutorials-ex2_0: 6.45 sec / 6.97 sec > Successfully remade target file `report_tests'. > Must remake target `test'. > Successfully remade target file `test'.

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Re: [petsc-dev] openmpi downloaded tarball broken ?
by Barry Smith 03 Jan '21

03 Jan '21

Any change sites might strip out "dangerous" shell scripts I reproduced the same problem several times with different versions of OpenMPI on the UTK xSDK machine. > On Jan 3, 2021, at 9:36 AM, Jed Brown <jed(a)jedbrown.org> wrote: > > I don't understand. > > $ wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.bz2 > --2021-01-03 08:35:08-- https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.bz2 > Resolving download.open-mpi.org (download.open-mpi.org) 143.204.26.61, 143.204.26.76, 143.204.26.58, ... > Connecting to download.open-mpi.org (download.open-mpi.org)|143.204.26.61|:443... connected. > HTTP request sent, awaiting response... 200 OK > Length: 10022171 (9.6M) [binary/octet-stream] > Saving to: ‘openmpi-4.1.0.tar.bz2’ > > openmpi-4.1.0.tar.bz2 100%[==================================>] 9.56M 46.6MB/s in 0.2s > > 2021-01-03 08:35:08 (46.6 MB/s) - ‘openmpi-4.1.0.tar.bz2’ saved [10022171/10022171] > > $ tar xf openmpi-4.1.0.tar.bz2 > $ file openmpi-4.1.0/configure > openmpi-4.1.0/configure: POSIX shell script, ASCII text executable, with very long lines > > Barry Smith <bsmith(a)petsc.dev> writes: > >> 4.1 is also missing ./configure but documentation clearly states you install openMPI with ./configure ! >> >>> On Jan 3, 2021, at 8:31 AM, Barry Smith <bsmith(a)petsc.dev> wrote: >>> >>> >>> $ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> >>> --2021-01-03 09:24:24-- https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> >>> Resolving download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)... 13.249.117.107, 13.249.117.91, 13.249.117.41, ... >>> Connecting to download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)|13.249.117.107|:443... connected. >>> HTTP request sent, awaiting response... 200 OK >>> Length: 17418534 (17M) [binary/octet-stream] >>> Saving to: ‘openmpi-4.0.3.tar.gz’ >>> >>> 100%[=======================================================================>] 17,418,534 49.1MB/s in 0.3s >>> >>> 2021-01-03 09:24:26 (49.1 MB/s) - ‘openmpi-4.0.3.tar.gz’ saved [17418534/17418534] >>> >>> ~ arch-fix-cuda-ccbin-wrong-arguments >>> $ cd petsc >>> ~/petsc (barry/2020-12-31/fix-cuda-ccbin-wrong-arguments>) arch-fix-cuda-ccbin-wrong-arguments >>> $ ./configure --download-openmpi=../openmpi-4.0.3.tar.gz --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-cuda --download-slepc >>> =============================================================================== >>> Configuring PETSc to compile on your system >>> =============================================================================== >>> ============================================================================================= ***** WARNING: F77 (set to /nfs/apps/spacks/2020-10-22/opt/spack/linux-centos7-x86_64/gcc-7.3.0/gcc-7.3.0-l use ./configure F77=$F77 if you really want to use that value ****** ============================================================================================= ============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports, or use the --download-make option to get the latest GNU make ***** ============================================================================================= ============================================================================================= It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org <http://www.valgrind.org/> Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure ============================================================================================= ============================================================================================= Running libtoolize on OPENMPI; this may take several minutes ============================================================================================= ============================================================================================= Running autoreconf on OPENMPI; this may take several minutes ============================================================================================= ******************************************************************************* >>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >>> ------------------------------------------------------------------------------- >>> Error running libtoolize or autoreconf on OPENMPI: Could not execute "[['/usr/bin/autoreconf', '--force', '--install']]": >>> autoreconf: 'configure.ac' or 'configure.in' is required >>> ******************************************************************************* >>> >>>

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false positive test
by Mark Adams 03 Jan '21

03 Jan '21

My test will fail if the gold output file is missing but otherwise it seems to always succeed. I just branched this from master. Any ideas? (base) 11:37 adams/landau-cleanup *= ~/Codes/petsc$ *rm* src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out remove src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out? y (base) 11:37 adams/landau-cleanup *= ~/Codes/petsc$ *touch* /Users/markadams/Codes/petsc/src/ts/utils/dmplexlandau/tutorials/output/ex2_0.out (base) 11:45 2 adams/landau-cleanup *= ~/Codes/petsc$ *make -f gmakefile --debug test search='ts_utils_dmplexlandau_tutorials-ex2_0'* GNU Make 3.81 Copyright (C) 2006 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program built for i386-apple-darwin11.3.0 Reading makefiles... Updating goal targets.... File `test' does not exist. File `report_tests' does not exist. File `starttime' does not exist. File `pre-clean' does not exist. Must remake target `pre-clean'. Using MAKEFLAGS: --debug=basic -- search=ts_utils_dmplexlandau_tutorials-ex2_0 Successfully remade target file `pre-clean'. Must remake target `starttime'. Successfully remade target file `starttime'. File `ts_utils_dmplexlandau_tutorials-ex2_0' does not exist. File `arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts' does not exist. Must remake target `arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts'. TEST arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts ok ts_utils_dmplexlandau_tutorials-ex2_0 ok diff-ts_utils_dmplexlandau_tutorials-ex2_0 Successfully remade target file `arch-macosx-gnu-g/tests/counts/ts_utils_dmplexlandau_tutorials-ex2_0.counts'. Must remake target `ts_utils_dmplexlandau_tutorials-ex2_0'. Successfully remade target file `ts_utils_dmplexlandau_tutorials-ex2_0'. Must remake target `report_tests'. # ------------- # Summary # ------------- # success 2/2 tests (100.0%) # failed 0/2 tests (0.0%) # todo 0/2 tests (0.0%) # skip 0/2 tests (0.0%) # # Wall clock time for tests: 7 sec # Approximate CPU time (not incl. build time): 6.97 sec # # Timing summary (actual test time / total CPU time): # ts_utils_dmplexlandau_tutorials-ex2_0: 6.45 sec / 6.97 sec Successfully remade target file `report_tests'. Must remake target `test'. Successfully remade target file `test'.

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Re: [petsc-dev] openmpi downloaded tarball broken ?
by Jed Brown 03 Jan '21

03 Jan '21

I don't understand. $ wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.bz2 --2021-01-03 08:35:08-- https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.0.tar.bz2 Resolving download.open-mpi.org (download.open-mpi.org) 143.204.26.61, 143.204.26.76, 143.204.26.58, ... Connecting to download.open-mpi.org (download.open-mpi.org)|143.204.26.61|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 10022171 (9.6M) [binary/octet-stream] Saving to: ‘openmpi-4.1.0.tar.bz2’ openmpi-4.1.0.tar.bz2 100%[==================================>] 9.56M 46.6MB/s in 0.2s 2021-01-03 08:35:08 (46.6 MB/s) - ‘openmpi-4.1.0.tar.bz2’ saved [10022171/10022171] $ tar xf openmpi-4.1.0.tar.bz2 $ file openmpi-4.1.0/configure openmpi-4.1.0/configure: POSIX shell script, ASCII text executable, with very long lines Barry Smith <bsmith(a)petsc.dev> writes: > 4.1 is also missing ./configure but documentation clearly states you install openMPI with ./configure ! > >> On Jan 3, 2021, at 8:31 AM, Barry Smith <bsmith(a)petsc.dev> wrote: >> >> >> $ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> >> --2021-01-03 09:24:24-- https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> >> Resolving download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)... 13.249.117.107, 13.249.117.91, 13.249.117.41, ... >> Connecting to download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)|13.249.117.107|:443... connected. >> HTTP request sent, awaiting response... 200 OK >> Length: 17418534 (17M) [binary/octet-stream] >> Saving to: ‘openmpi-4.0.3.tar.gz’ >> >> 100%[=======================================================================>] 17,418,534 49.1MB/s in 0.3s >> >> 2021-01-03 09:24:26 (49.1 MB/s) - ‘openmpi-4.0.3.tar.gz’ saved [17418534/17418534] >> >> ~ arch-fix-cuda-ccbin-wrong-arguments >> $ cd petsc >> ~/petsc (barry/2020-12-31/fix-cuda-ccbin-wrong-arguments>) arch-fix-cuda-ccbin-wrong-arguments >> $ ./configure --download-openmpi=../openmpi-4.0.3.tar.gz --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-cuda --download-slepc >> =============================================================================== >> Configuring PETSc to compile on your system >> =============================================================================== >> ============================================================================================= ***** WARNING: F77 (set to /nfs/apps/spacks/2020-10-22/opt/spack/linux-centos7-x86_64/gcc-7.3.0/gcc-7.3.0-l use ./configure F77=$F77 if you really want to use that value ****** ============================================================================================= ============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports, or use the --download-make option to get the latest GNU make ***** ============================================================================================= ============================================================================================= It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org <http://www.valgrind.org/> Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure ============================================================================================= ============================================================================================= Running libtoolize on OPENMPI; this may take several minutes ============================================================================================= ============================================================================================= Running autoreconf on OPENMPI; this may take several minutes ============================================================================================= ******************************************************************************* >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): >> ------------------------------------------------------------------------------- >> Error running libtoolize or autoreconf on OPENMPI: Could not execute "[['/usr/bin/autoreconf', '--force', '--install']]": >> autoreconf: 'configure.ac' or 'configure.in' is required >> ******************************************************************************* >> >>

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Re: [petsc-dev] openmpi downloaded tarball broken ?
by Barry Smith 03 Jan '21

03 Jan '21

4.1 is also missing ./configure but documentation clearly states you install openMPI with ./configure ! > On Jan 3, 2021, at 8:31 AM, Barry Smith <bsmith(a)petsc.dev> wrote: > > > $ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> > --2021-01-03 09:24:24-- https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz <https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz> > Resolving download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)... 13.249.117.107, 13.249.117.91, 13.249.117.41, ... > Connecting to download.open-mpi.org <http://download.open-mpi.org/> (download.open-mpi.org <http://download.open-mpi.org/>)|13.249.117.107|:443... connected. > HTTP request sent, awaiting response... 200 OK > Length: 17418534 (17M) [binary/octet-stream] > Saving to: ‘openmpi-4.0.3.tar.gz’ > > 100%[=======================================================================>] 17,418,534 49.1MB/s in 0.3s > > 2021-01-03 09:24:26 (49.1 MB/s) - ‘openmpi-4.0.3.tar.gz’ saved [17418534/17418534] > > ~ arch-fix-cuda-ccbin-wrong-arguments > $ cd petsc > ~/petsc (barry/2020-12-31/fix-cuda-ccbin-wrong-arguments>) arch-fix-cuda-ccbin-wrong-arguments > $ ./configure --download-openmpi=../openmpi-4.0.3.tar.gz --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-cuda --download-slepc > =============================================================================== > Configuring PETSc to compile on your system > =============================================================================== > ============================================================================================= ***** WARNING: F77 (set to /nfs/apps/spacks/2020-10-22/opt/spack/linux-centos7-x86_64/gcc-7.3.0/gcc-7.3.0-l use ./configure F77=$F77 if you really want to use that value ****** ============================================================================================= ============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports, or use the --download-make option to get the latest GNU make ***** ============================================================================================= ============================================================================================= It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org <http://www.valgrind.org/> Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure ============================================================================================= ============================================================================================= Running libtoolize on OPENMPI; this may take several minutes ============================================================================================= ============================================================================================= Running autoreconf on OPENMPI; this may take several minutes ============================================================================================= ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): > ------------------------------------------------------------------------------- > Error running libtoolize or autoreconf on OPENMPI: Could not execute "[['/usr/bin/autoreconf', '--force', '--install']]": > autoreconf: 'configure.ac' or 'configure.in' is required > ******************************************************************************* > >

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openmpi downloaded tarball broken ?
by Barry Smith 03 Jan '21

03 Jan '21

$ wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz --2021-01-03 09:24:24-- https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.3.tar.gz Resolving download.open-mpi.org (download.open-mpi.org) 13.249.117.107, 13.249.117.91, 13.249.117.41, ... Connecting to download.open-mpi.org (download.open-mpi.org)|13.249.117.107|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 17418534 (17M) [binary/octet-stream] Saving to: ‘openmpi-4.0.3.tar.gz’ 100%[=======================================================================>] 17,418,534 49.1MB/s in 0.3s 2021-01-03 09:24:26 (49.1 MB/s) - ‘openmpi-4.0.3.tar.gz’ saved [17418534/17418534] ~ arch-fix-cuda-ccbin-wrong-arguments $ cd petsc ~/petsc (barry/2020-12-31/fix-cuda-ccbin-wrong-arguments>) arch-fix-cuda-ccbin-wrong-arguments $ ./configure --download-openmpi=../openmpi-4.0.3.tar.gz --with-cc=gcc --with-cxx=g++ --with-fc=gfortran --with-cuda --download-slepc =============================================================================== Configuring PETSc to compile on your system =============================================================================== ============================================================================================= ***** WARNING: F77 (set to /nfs/apps/spacks/2020-10-22/opt/spack/linux-centos7-x86_64/gcc-7.3.0/gcc-7.3.0-l use ./configure F77=$F77 if you really want to use that value ****** ============================================================================================= ============================================================================================= ***** WARNING: You have a version of GNU make older than 4.0. It will work, but may not support all the parallel testing options. You can install the latest GNU make with your package manager, such as brew or macports, or use the --download-make option to get the latest GNU make ***** ============================================================================================= ============================================================================================= It appears you do not have valgrind installed on your system. We HIGHLY recommend you install it from www.valgrind.org Or install valgrind-devel or equivalent using your package manager. Then rerun ./configure ============================================================================================= ============================================================================================= Running libtoolize on OPENMPI; this may take several minutes ============================================================================================= ============================================================================================= Running autoreconf on OPENMPI; this may take several minutes ============================================================================================= ******************************************************************************* UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details): ------------------------------------------------------------------------------- Error running libtoolize or autoreconf on OPENMPI: Could not execute "[['/usr/bin/autoreconf', '--force', '--install']]": autoreconf: 'configure.ac' or 'configure.in' is required *******************************************************************************

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Re: [petsc-dev] checkbadSource issue
by Barry Smith 01 Jan '21

01 Jan '21

https://gitlab.com/petsc/petsc/-/merge_requests/3532 <https://gitlab.com/petsc/petsc/-/merge_requests/3532> attempts to remove bash specific syntax from checkbadSource. > On Dec 31, 2020, at 3:18 AM, Jose E. Roman <jroman(a)dsic.upv.es> wrote: > > I am getting the same in some machines. I don't think this is due to a recent change. > > In the pipeline, it is run as > $ make checkbadSource SHELL=bash > which solves the issue. > > > On the other hand, in the 'checksource' job in the pipelines, there are errors (probably not important): > gmakefile.test:100: arch-linux-c-debug/tests/testfiles: No such file or directory > gmakefile:67: arch-linux-c-debug/lib/petsc/conf/files: No such file or directory > > Jose > >> El 31 dic 2020, a las 9:30, Stefano Zampini <stefano.zampini(a)gmail.com> escribió: >> >> Just rebased my MR over master >> >> zampins@vulture:~/Devel/petsc$ make checkbadSource >> /bin/sh: 1: let: not found >> /bin/sh: 2: [: -gt: unexpected operator >> /bin/sh: 6: test: Illegal number: ! >> /home/zampins/Devel/petsc/lib/petsc/conf/rules:660: recipe for target 'checkbadSource' failed >> make[1]: *** [checkbadSource] Error 2 >> GNUmakefile:17: recipe for target 'checkbadSource' failed >> make: *** [checkbadSource] Error 2 >> >> -- >> Stefano >

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Re: [petsc-dev] Testing seems broken in master
by Barry Smith 01 Jan '21

01 Jan '21

Matt, This is in https://gitlab.com/petsc/petsc/-/merge_requests/3531/pipelines <https://gitlab.com/petsc/petsc/-/merge_requests/3531/pipelines> ready for review. Barry > On Dec 31, 2020, at 1:02 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Thu, Dec 31, 2020 at 1:48 PM Barry Smith <bsmith(a)petsc.dev <mailto:[email protected]>> wrote: > > So the programs output changes and should no longer match that in the output/* file yet the test harness does not error with a statement that the two outputs do not match? > > I noticed the gmakegentest.py is not being run before it runs the test? Does this mean it is just running all the old stuff which does match fine? > > Then either how petscdiff is called by the test harness has changed or petscdiff has changed and does not detect changes anymore > > BTW: I always use -f ./gmakefile.test test not just the gmakefile > > All the PETSc changes are trivial and can be seen with a simple diff, it is hard to believe they would cause this behavior but I guess they must. > > You can go to PETSC_ARCH/tests/snes/tests and run the ex13 shell script directly. > > It is the sed problem: > > master *$:/PETSc3/petsc/petsc-dev$ /PETSc3/petsc/petsc-dev/lib/petsc/bin/petscdiff /PETSc3/petsc/petsc-dev/src/snes/tests/output/ex13_bench.out ex13_bench.tmp > > sed: 1: "s/\033[1;31m//g": unbalanced brackets ([]) > sed: 1: "s/\033[0;39m\033[0;49m//g": unbalanced brackets ([]) > sed: 1: "s/\033[1;31m//g": unbalanced brackets ([]) > sed: 1: "s/\033[0;39m\033[0;49m//g": unbalanced brackets ([]) > > The error was getting eaten. > > This is in current master. Is it fixed in a branch? > > Matt > > Barry > > >> On Dec 31, 2020, at 12:38 PM, Matthew Knepley <knepley(a)gmail.com <mailto:[email protected]>> wrote: >> >> I just pulled master, and simple alterations to tests do not produce a failure: >> >> master *$:/PETSc3/petsc/petsc-dev$ PETSC_ARCH=arch-master-debug make -f ./gmakefile test search="snes_tests-ex13_bench" TIMEOUT=5000 EXTRA_OPTIONS="-dm_ >> refine 0" >> Using MAKEFLAGS: EXTRA_OPTIONS=-dm_refine 0 TIMEOUT=5000 search=snes_tests-ex13_bench >> TEST arch-master-debug/tests/counts/snes_tests-ex13_bench.counts >> ok snes_tests-ex13_bench >> ok diff-snes_tests-ex13_bench >> >> I check that the runs produce different output when done manually. >> >> Scott and Barry, could this be related to changed to testing? >> >> Thanks, >> >> Matt >> >> -- >> 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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Re: [petsc-dev] ASM for each field solve on GPUs
by Mark Adams 31 Dec '20

31 Dec '20

On Thu, Dec 31, 2020 at 7:42 PM Barry Smith <bsmith(a)petsc.dev> wrote: > > Mark, > > PCFIELDSPLIT PCFieldSplitSetDefaults uses the block size of the matrix > to determine the number of splits. > Yes > > It could be that the matrices returned by PCASM have a default block > size of 1 (instead of inheriting the block size of the matrix the sub > matrix was obtained with). > > MatCreateSubMatrices_MPIAIJ_Local() has err = > MatSetBlockSizes(submats[i],rbs,cbs);CHKERRQ(ierr); where rbs and cbs get > their block sizes from the IS. You would need to dig into the code, with > the debugger? to see if the block size is propagated to the sub matrices > and why not. It should be, but likely that is never specifically tested. > > I think it is working now. Still a lot more work to do but Stefano and Jed helped me get logic the way I want with a separate scalar matrix for each field. So I have the block diagonal that I want and it looks like I am doing solve on each of the two blocks in my example and it is an exact solver. Thanks, > > Barry > > > On Dec 31, 2020, at 7:40 AM, Mark Adams <mfadams(a)lbl.gov> wrote: > > Humm, I have two fields (Nf) here: > > /usr/local/Cellar/mpich/3.3.2_1/bin/mpiexec -n 1 ./ex2 -ex2_test_type > spitzer -ex2_connor_e_field_units -dm_landau_Ez 0 -petscspace_degree 3 > -dm_landau_type p4est -dm_landau_ion_masses 1 -dm_landau_ion_charges 1 > -dm_landau_thermal_temps 4,4 -dm_landau_n 1,1 -ts_monitor -ts_adapt_monitor > -snes_rtol 1.e-14 -snes_stol 1.e-14 -snes_monitor -snes_converged_reason > -snes_max_it 15 -ts_type arkimex -ts_exact_final_time stepover > -ts_arkimex_type 1bee -ts_max_snes_failures -1 -ts_rtol 1e-3 -ts_dt .1e-1 > -ts_adapt_clip .25,1.1 -ts_max_time 100 -ts_max_steps 1 > -ts_adapt_scale_solve_failed 0.75 -ts_adapt_time_step_increase_delay 5 > -pc_type lu -ksp_type preonly -dm_landau_amr_levels_max 8 > -dm_landau_amr_post_refine 0 -dm_landau_domain_radius 5 -ex2_plot_dt 1 > -info :dm -ts_adapt_dt_min 1e-4 -ts_adapt_dt_max 1. -dm_preallocate_only > -ex2_impurity_source_type pulse -ex2_pulse_start_time 32 > -ex2_pulse_width_time 15 -ex2_pulse_rate 2e+0 -ex2_t_cold 1 > -dm_landau_device_type cpu -pc_type asm -sub_pc_type fieldsplit > -sub_pc_fieldsplit_type additive -sub_fieldsplit_0_pc_type lu -ksp_monitor > [0] ProcessOptions(): num_species set to number of thermal temps provided > (2) > masses: e= 9.109e-31; ions in proton mass units: 1.000e+00 > 0.000e+00 ... > charges: e=-1.602e-19; charges in elementary units: 1.000e+00 > 0.000e+00 > thermal T (K): e= 4.642e+07 i= 4.642e+07 imp= 0.000e+00. v_0= 2.652e+07 > n_0= 1.000e+20 t_0= 4.630e-05 domain= 5.000e+00 > [0] ProcessREOptions(): Num electrons from ions=1., T_cold= 1.160e+07, ion > potential= 1.500e+01, E_z= 0.000e+00 v_0= 2.652e+07 > CalculateE j0=0. Ec = 0.0509908 > [0] DMGetDMSNES(): Creating new DMSNES > [0] DMGetDMTS(): Creating new DMTS > [0] DMGetDMSNESWrite(): Copying DMSNES due to write > 0 TS dt 0.01 time 0. > > *0) species-0: charge density= -1.6022862392985e+01 z-momentum= > -1.4067414979736e-19 energy= 9.6063873494138e+04 0) species-1: charge > density= 1.6029890912678e+01 z-momentum= -8.1631830255319e-18 energy= > 9.6333618295472e+04* > 0) Total: charge density= 7.0285196929767e-03, momentum= > -8.3038571753292e-18, energy= 1.9239749178961e+05 (m_i[0]/m_e = 1835.47, > 50 cells) > testSpitzer 0) time= 0.000e+00 n_e= 1.000e+00 E= 0.000e+00 J= > -1.495e-07 J_re= -0.000e+00 0 % Te_kev= 3.995e+00 Z_eff=1. E/J to eta > ratio=-0. (diff=1e+10) constant E > [0] DMGetDMKSP(): Creating new DMKSP > [0]FormLandau: 800 IPs, 50 cells, totDim=32, Nb=16, Nq=16, > elemMatSize=1024, dim=2, Tab: Nb=16 *Nf=2 *Np=16 cdim=2 N=896 N+hang=1176 > 0 SNES Function norm 4.974988592014e-03 > [0]PETSC ERROR: --------------------- Error Message > -------------------------------------------------------------- > [0]PETSC ERROR: Petsc has generated inconsistent data > > *[0]PETSC ERROR: Unhandled case, must have at least two fields, not 1*[0]PETSC > ERROR: See https://www.mcs.anl.gov/petsc/documentation/faq.html for > trouble shooting. > [0]PETSC ERROR: Petsc Development GIT revision: v3.14.2-353-gc57b1f101b > GIT Date: 2020-12-27 11:51:24 -0600 > [0]PETSC ERROR: ./ex2 on a arch-macosx-gnu-g named MarksMac-302.local by > markadams Thu Dec 31 08:35:49 2020 > [0]PETSC ERROR: Configure options > --with-mpi-dir=/usr/local/Cellar/mpich/3.3.2_1 COPTFLAGS="-g -O0" > CXXOPTFLAGS="-g -O0" --download-metis=1 --download-parmetis=1 > --download-kokkos=1 --download-kokkos-kernels=1 --download-p4est=1 > --with-zlib=1 --with-make-np=4 --download-hdf5=1 -with-cuda=0 --with-x=0 > --with-debugging=1 PETSC_ARCH=arch-macosx-gnu-g --with-64-bit-indices=0 > --with-openmp=0 --with-ctable=0 > [0]PETSC ERROR: #1 PCFieldSplitSetDefaults() line 571 in > /Users/markadams/Codes/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c > [0]PETSC ERROR: #2 PCSetUp_FieldSplit() line 614 in > /Users/markadams/Codes/petsc/src/ksp/pc/impls/fieldsplit/fieldsplit.c > [0]PETSC ERROR: #3 PCSetUp() line 1015 in > /Users/markadams/Codes/petsc/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #4 KSPSetUp() line 406 in > /Users/markadams/Codes/petsc/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #5 PCSetUpOnBlocks_ASM() line 437 in > /Users/markadams/Codes/petsc/src/ksp/pc/impls/asm/asm.c > [0]PETSC ERROR: #6 PCSetUpOnBlocks() line 1046 in > /Users/markadams/Codes/petsc/src/ksp/pc/interface/precon.c > [0]PETSC ERROR: #7 KSPSetUpOnBlocks() line 214 in > /Users/markadams/Codes/petsc/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #8 KSPSolve_Private() line 727 in > /Users/markadams/Codes/petsc/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #9 KSPSolve() line 963 in > /Users/markadams/Codes/petsc/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: #10 SNESSolve_NEWTONLS() line 225 in > /Users/markadams/Codes/petsc/src/snes/impls/ls/ls.c > [0]PETSC ERROR: #11 SNESSolve() line 4563 in > /Users/markadams/Codes/petsc/src/snes/interface/snes.c > [0]PETSC ERROR: #12 TSStep_ARKIMEX() line 845 in > /Users/markadams/Codes/petsc/src/ts/impls/arkimex/arkimex.c > [0]PETSC ERROR: #13 TSStep() line 3771 in > /Users/markadams/Codes/petsc/src/ts/interface/ts.c > [0]PETSC ERROR: #14 TSSolve() line 4168 in > /Users/markadams/Codes/petsc/src/ts/interface/ts.c > [0]PETSC ERROR: #15 main() line 774 in ex2.c > [0]PETSC ERROR: PETSc Option Table entries: > [0]PETSC ERROR: -dm_landau_amr_levels_max 8 > [0]PETSC ERROR: -dm_landau_amr_post_refine 0 > [0]PETSC ERROR: -dm_landau_device_type cpu > [0]PETSC ERROR: -dm_landau_domain_radius 5 > [0]PETSC ERROR: -dm_landau_Ez 0 > [0]PETSC ERROR: -dm_landau_ion_charges 1 > [0]PETSC ERROR: -dm_landau_ion_masses 1 > [0]PETSC ERROR: -dm_landau_n 1,1 > [0]PETSC ERROR: -dm_landau_thermal_temps 4,4 > [0]PETSC ERROR: -dm_landau_type p4est > [0]PETSC ERROR: -dm_preallocate_only > [0]PETSC ERROR: -ex2_connor_e_field_units > [0]PETSC ERROR: -ex2_impurity_source_type pulse > [0]PETSC ERROR: -ex2_plot_dt 1 > [0]PETSC ERROR: -ex2_pulse_rate 2e+0 > [0]PETSC ERROR: -ex2_pulse_start_time 32 > [0]PETSC ERROR: -ex2_pulse_width_time 15 > [0]PETSC ERROR: -ex2_t_cold 1 > [0]PETSC ERROR: -ex2_test_type spitzer > [0]PETSC ERROR: -info :dm > [0]PETSC ERROR: -ksp_monitor > [0]PETSC ERROR: -ksp_type preonly > [0]PETSC ERROR: -pc_type asm > [0]PETSC ERROR: -petscspace_degree 3 > [0]PETSC ERROR: -snes_converged_reason > [0]PETSC ERROR: -snes_max_it 15 > [0]PETSC ERROR: -snes_monitor > [0]PETSC ERROR: -snes_rtol 1.e-14 > [0]PETSC ERROR: -snes_stol 1.e-14 > [0]PETSC ERROR: -sub_fieldsplit_0_pc_type lu > [0]PETSC ERROR: -sub_pc_fieldsplit_type additive > [0]PETSC ERROR: -sub_pc_type fieldsplit > [0]PETSC ERROR: -ts_adapt_clip .25,1.1 > [0]PETSC ERROR: -ts_adapt_dt_max 1. > [0]PETSC ERROR: -ts_adapt_dt_min 1e-4 > [0]PETSC ERROR: -ts_adapt_monitor > [0]PETSC ERROR: -ts_adapt_scale_solve_failed 0.75 > [0]PETSC ERROR: -ts_adapt_time_step_increase_delay 5 > [0]PETSC ERROR: -ts_arkimex_type 1bee > [0]PETSC ERROR: -ts_dt .1e-1 > [0]PETSC ERROR: -ts_exact_final_time stepover > [0]PETSC ERROR: -ts_max_snes_failures -1 > [0]PETSC ERROR: -ts_max_steps 1 > [0]PETSC ERROR: -ts_max_time 100 > [0]PETSC ERROR: -ts_monitor > [0]PETSC ERROR: -ts_rtol 1e-3 > [0]PETSC ERROR: -ts_type arkimex > [0]PETSC > > On Thu, Dec 31, 2020 at 12:30 AM Jed Brown <jed(a)jedbrown.org> wrote: > >> Mark Adams <mfadams(a)lbl.gov> writes: >> >> > I think the first thing that I need to do is get ASM working on the CPU >> in >> > my code as a direct solver. >> > >> > FieldSplit was mentioned the way to do this. How would I do that? >> >> -pc_type asm -sub_pc_type fieldsplit -sub_pc_fieldsplit_type additive >> -sub_fieldsplit_0_pc_type lu >> > >

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