Re: [firedrake] [petsc-maint] Firedrake - PETSC CONFIGURATION CRASH
On Fri, Apr 22, 2022 at 10:58 AM John Snyder via petsc-maint < petsc-maint@mcs.anl.gov> wrote:
Satish, I must be an idiot. I tried using your potential fix, But I cannot find the branch? I looked in fired rack and PETSc GitHub but searching I was unable to locate the repo. I tried:
Notice that this is cloning the FIredrake fork of PETSc, which probably does not have this branch. I have added them to this thread. Thanks, Matt
... 2022-04-22 09:28:47,265 DEBUG Running command 'git clone -q --recursive https://github.com/firedrakeproject/petsc.git' 2022-04-22 09:30:37,982 DEBUG 2022-04-22 09:30:37,991 INFO Successfully cloned repository petsc. 2022-04-22 09:30:38,001 DEBUG Old path '/data/gpfs/Users/l1057678/firedrake-new/build/src' 2022-04-22 09:30:38,001 DEBUG Pushing path '/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc' 2022-04-22 09:30:38,001 INFO Checking out branch balay/fix-executables-search-path 2022-04-22 09:30:38,001 DEBUG Running command 'git checkout -q balay/fix-executables-search-path' 2022-04-22 09:30:38,031 DEBUG error: pathspec 'balay/fix-executables-search-path' did not match any file(s) known to git.
2022-04-22 09:30:38,031 ERROR Failed to check out branch balay/fix-executables-search-path 2022-04-22 09:30:38,031 DEBUG Popping path '/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc' 2022-04-22 09:30:38,031 DEBUG New path '/data/gpfs/Users/l1057678/firedrake-new/build/src’
I used the following: */hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin/python3 ./firedrake-install --no-package-manager --venv-name build --tinyasm --disable-ssh --minimal-petsc --slepc --documentation-dependencies --install thetis --install gusto --install icepack --install irksome --install femlium --package-branch petsc balay/fix-executables-search-path --package-branch slepc balay/fix-executables-search-path*
What am I doing wrong?
Best Regards, John P.S. Thank you for all you assistance.
On Apr 21, 2022, at 1:24 PM, Satish Balay <balay@mcs.anl.gov> wrote:
I pushed a potential fix [off release] in branch balay/fix-executables-search-path - can you try it?
[if you need this fix on main branch - you can merge it over locally - and test]
Satish
On Thu, 21 Apr 2022, Satish Balay via petsc-maint wrote:
--with-executables-search-path=/hrtc/apps/devtools/cmake/x86_64/3.8.2/bin:/hrtc/apps/scripting/anaconda3/x86_64/2020.02/sbin:/hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin:/hrtc/apps/mpi/openmpi/4.0.1/RDHPC/gcc/8.2.0/bin:/apps/gcc/8.2.0/x86_64/libexec/gcc/x86_64-pc-linux-gnu/8.2.0:/apps/gcc/8.2.0/x86_64/bin:.:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/apps/slurm/x86/20.02.0/bin:/apps/slurm/x86/20.02.0/sbin:/usr/bin
Hm - did this option ever work? [I don't remember seeing this in a very long time
I suspect its expecting a list - in python notation [and not in PATH notation]. So probably needs fixing. But do you need this option?
Satish
On Thu, 21 Apr 2022, John Snyder via petsc-maint wrote:
Team, Please note, firedrake installation fails !!!
Configuring PETSc to compile on your system
============================================================================================= TESTING: configureExternalPackagesDir from config.framework(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/BuildSystem/config/framework.py:1030) TESTING: configureDebuggers from config.utilities.debuggers(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/BuildSystem/config/utilities/debuggers.py:20) TESTING: configureDirectories from PETSc.options.petscdir(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/PETSc/options/petscdir.py:22)
******************************************************************************* CONFIGURATION CRASH (Please send configure.log to petsc-maint@mcs.anl.gov<mailto:petsc-maint@mcs.anl.gov <petsc-maint@mcs.anl.gov>>)
===================================================================================================================== This failure during install is from: export PETSC_CONFIGURE_OPTIONS="--with-cc=mpicc --CC=mpicc --CXX=mpic++ --FC=mpifort --download-openblas --with-executables-search-path=${PATH}" --download-ml --download-mpich --download-pastix --download-ptscotch --with-cxx-dialect=C++11 --download-eigen=/data/gpfs/Users/l1057678/firedrake-spack/firedrake/src/eigen-3.3.3.tgz --with-fortran-bindings=0 --download-cmake --with-debugging=0 --download-hdf5 --download-superlu_dist --download-netcdf --with-c2html=0 --download-suitesparse --download-scalapack --download-hypre --download-pnetcdf --with-shared-libraries=1 --download-hwloc --with-bison-exec=/usr/bin/bison
/hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin/python3 ./firedrake-install --no-package-manager --venv-name build --tinyasm --disable-ssh --minimal-petsc --slepc --documentation-dependencies --install thetis --install gusto --install icepack --install irksome --install femlium --package-branch petsc connorjward/merge-upstream --package-branch slepc connorjward/merge-upstream
Please see attached firedrake-install.log and petsc configure.log
Best Regard, John
P.S. Any and all assistance is greatly appreciated.
-- 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/>
Dear John, As Matt says, the Firedrake installer will use the Firedrake fork of PETSc. To use the main PETSc repo you need to build PETSc outside Firedrake, and then tell the Firedrake installer about it. You do that as follows: 1. Clone the main PETSc repo and configure and build using their instructions. You checkout the branch you want before configuring. Firedrake depends on a particular set of PETSc configure options being set. You access this list of options by running: python3 firedrake-install --show-petsc-configure-options 1. Set PETSC_DIR and PETSC_ARCH 2. Run firedrake-install passing the --honour-petsc-path option. Note the spelling of “honour”. If you’re mucking about inside PETSc, you probably want to install Firedrake with external PETSc any event, even if the branches you want are on our fork. Cheers, David -- Dr David A. Ham Reader in Computational Mathematics Department of Mathematics Imperial College London From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Matthew Knepley <knepley@gmail.com> Date: Saturday, 23 April 2022 at 01:03 To: John Snyder <b17jps@me.com> Cc: firedrake <firedrake@imperial.ac.uk>, petsc-maint <petsc-maint@mcs.anl.gov> Subject: Re: [firedrake] [petsc-maint] Firedrake - PETSC CONFIGURATION CRASH On Fri, Apr 22, 2022 at 10:58 AM John Snyder via petsc-maint <petsc-maint@mcs.anl.gov<mailto:petsc-maint@mcs.anl.gov>> wrote: Satish, I must be an idiot. I tried using your potential fix, But I cannot find the branch? I looked in fired rack and PETSc GitHub but searching I was unable to locate the repo. I tried: Notice that this is cloning the FIredrake fork of PETSc, which probably does not have this branch. I have added them to this thread. Thanks, Matt ... 2022-04-22 09:28:47,265 DEBUG Running command 'git clone -q --recursive https://github.com/firedrakeproject/petsc.git' 2022-04-22 09:30:37,982 DEBUG 2022-04-22 09:30:37,991 INFO Successfully cloned repository petsc. 2022-04-22 09:30:38,001 DEBUG Old path '/data/gpfs/Users/l1057678/firedrake-new/build/src' 2022-04-22 09:30:38,001 DEBUG Pushing path '/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc' 2022-04-22 09:30:38,001 INFO Checking out branch balay/fix-executables-search-path 2022-04-22 09:30:38,001 DEBUG Running command 'git checkout -q balay/fix-executables-search-path' 2022-04-22 09:30:38,031 DEBUG error: pathspec 'balay/fix-executables-search-path' did not match any file(s) known to git. 2022-04-22 09:30:38,031 ERROR Failed to check out branch balay/fix-executables-search-path 2022-04-22 09:30:38,031 DEBUG Popping path '/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc' 2022-04-22 09:30:38,031 DEBUG New path '/data/gpfs/Users/l1057678/firedrake-new/build/src’ I used the following: /hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin/python3 ./firedrake-install --no-package-manager --venv-name build --tinyasm --disable-ssh --minimal-petsc --slepc --documentation-dependencies --install thetis --install gusto --install icepack --install irksome --install femlium --package-branch petsc balay/fix-executables-search-path --package-branch slepc balay/fix-executables-search-path What am I doing wrong? Best Regards, John P.S. Thank you for all you assistance. On Apr 21, 2022, at 1:24 PM, Satish Balay <balay@mcs.anl.gov<mailto:balay@mcs.anl.gov>> wrote: I pushed a potential fix [off release] in branch balay/fix-executables-search-path - can you try it? [if you need this fix on main branch - you can merge it over locally - and test] Satish On Thu, 21 Apr 2022, Satish Balay via petsc-maint wrote: --with-executables-search-path=/hrtc/apps/devtools/cmake/x86_64/3.8.2/bin:/hrtc/apps/scripting/anaconda3/x86_64/2020.02/sbin:/hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin:/hrtc/apps/mpi/openmpi/4.0.1/RDHPC/gcc/8.2.0/bin:/apps/gcc/8.2.0/x86_64/libexec/gcc/x86_64-pc-linux-gnu/8.2.0:/apps/gcc/8.2.0/x86_64/bin:.:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/apps/slurm/x86/20.02.0/bin:/apps/slurm/x86/20.02.0/sbin:/usr/bin Hm - did this option ever work? [I don't remember seeing this in a very long time I suspect its expecting a list - in python notation [and not in PATH notation]. So probably needs fixing. But do you need this option? Satish On Thu, 21 Apr 2022, John Snyder via petsc-maint wrote: Team, Please note, firedrake installation fails !!! Configuring PETSc to compile on your system ============================================================================================= TESTING: configureExternalPackagesDir from config.framework(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/BuildSystem/config/framework.py:1030) TESTING: configureDebuggers from config.utilities.debuggers(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/BuildSystem/config/utilities/debuggers.py:20) TESTING: configureDirectories from PETSc.options.petscdir(/data/gpfs/Users/l1057678/firedrake-new/build/src/petsc/config/PETSc/options/petscdir.py:22) ******************************************************************************* CONFIGURATION CRASH (Please send configure.log to petsc-maint@mcs.anl.gov<mailto:petsc-maint@mcs.anl.gov><mailto:petsc-maint@mcs.anl.gov>) ===================================================================================================================== This failure during install is from: export PETSC_CONFIGURE_OPTIONS="--with-cc=mpicc --CC=mpicc --CXX=mpic++ --FC=mpifort --download-openblas --with-executables-search-path=${PATH}" --download-ml --download-mpich --download-pastix --download-ptscotch --with-cxx-dialect=C++11 --download-eigen=/data/gpfs/Users/l1057678/firedrake-spack/firedrake/src/eigen-3.3.3.tgz --with-fortran-bindings=0 --download-cmake --with-debugging=0 --download-hdf5 --download-superlu_dist --download-netcdf --with-c2html=0 --download-suitesparse --download-scalapack --download-hypre --download-pnetcdf --with-shared-libraries=1 --download-hwloc --with-bison-exec=/usr/bin/bison /hrtc/apps/scripting/anaconda3/x86_64/2020.02/bin/python3 ./firedrake-install --no-package-manager --venv-name build --tinyasm --disable-ssh --minimal-petsc --slepc --documentation-dependencies --install thetis --install gusto --install icepack --install irksome --install femlium --package-branch petsc connorjward/merge-upstream --package-branch slepc connorjward/merge-upstream Please see attached firedrake-install.log and petsc configure.log Best Regard, John P.S. Any and all assistance is greatly appreciated. -- 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/>
Team, I am struggling installing firedrake….I almost have it ….firedrake-update is failing. Unable to locate libsupermesh-c.h firedrake/cython/supermeshimpl.c:711:10: fatal error: libsupermesh-c.h: No such file or directory #include "libsupermesh-c.h" ^~~~~~~~~~~~~~~~~~ compilation terminated. Any help is greatly appreciated. Best Regards, John P.S. More info: (build) [l1057678@rdhpc-n1 build]$ python3 Python 3.7.6 (default, Jan 8 2020, 19:59:22) [GCC 7.3.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.
help("modules")
Please wait a moment while I gather a list of all available modules... /apps/firedrake/build/lib/python3.7/site-packages/IPython/kernel/__init__.py:13: ShimWarning: The `IPython.kernel` package has been deprecated since IPython 4.0.You should import from ipykernel or jupyter_client instead. "You should import from ipykernel or jupyter_client instead.", ShimWarning) /hrtc/apps/scripting/anaconda3/x86_64/2020.02/lib/python3.7/pkgutil.py:107: VisibleDeprecationWarning: zmq.eventloop.minitornado is deprecated in pyzmq 14.0 and will be removed. Install tornado itself to use zmq with the tornado IOLoop. yield from walk_packages(path, info.name+'.', onerror) Cython base64 itertools quopri FIAT bdb jedi random IPython benchmarks json re PIL binascii jsonschema readline __future__ binhex jupyter reprlib _abc bisect jupyter_client requests _ast builtins jupyter_core resource _asyncio bz2 keyword rlcompleter _bisect cProfile kiwisolver rmagic _blake2 cached_property lazy_object_proxy runpy _bootlocale cachetools lib2to3 sched _bz2 calendar libHYPRE secrets _codecs certifi libhdf5 select _codecs_cn cgen libhdf5_hl selectors _codecs_hk cgi libmetis setup _codecs_iso2022 cgitb libml setuptools _codecs_jp charset_normalizer libparmetis shelve _codecs_kr chunk libpetsc shlex _codecs_tw cmath libsuperlu_dist shutil _collections cmd libsuperlu_dist_fortran signal _collections_abc code linecache site _compat_pickle codecs locale six _compression codeop logging smtpd _contextvars codepy loopy smtplib _crypt coffee lzma sndhdr _csv collections macpath socket _ctypes colorama mailbox socketserver _ctypes_test colorsys mailcap spwd _curses compileall mako sqlite3 _curses_panel concurrent markupsafe sre_compile _datetime configparser marshal sre_constants _decimal contextlib math sre_parse _distutils_hack contextvars matplotlib ssl _dummy_thread copy matplotlib_inline stat _elementtree copyreg mccabe statistics _functools coverage mimetypes storemagic _hashlib crypt mmap string _heapq csv modulefinder stringprep _imp ctypes mpi4py struct _io curses mpmath subprocess _json cycler multidict sunau _locale cython multiprocessing symbol _lsprof cythonmagic nbformat symengine _lzma dataclasses nbval sympy _markupbase datetime nest_asyncio sympyprinting _md5 dateutil netrc symtable _multibytecodec dbm networkx sys _multiprocessing debugpy nis sysconfig _opcode decimal nntplib syslog _operator decorator ntpath tabnanny _osx_support difflib nturl2path tarfile _pickle dill numbers telnetlib _posixsubprocess dis numpy tempfile _py_abc distutils numpy_adjoint termios _pydecimal doctest opcode test _pyio dolfin_adjoint operator tests _pyrsistent_version dolfin_adjoint_common optparse textwrap _pytest dummy_threading os this _queue email ossaudiodev threading _random encodings packaging time _sha1 ensurepip parser timeit _sha256 entrypoints parso tkinter _sha3 enum pathlib token _sha512 errno pdb tokenize _signal execnet petsc4py toml _sitebuiltins fastjsonschema pexpect tomli _socket faulthandler pickle tornado _sqlite3 fcntl pickleshare trace _sre fenics_adjoint pickletools traceback _ssl filecmp pip tracemalloc _stat fileinput pipes traitlets _string finat pkg_resources tsfc _strptime firedrake_adjoint pkgconfig tty _struct flake8 pkgutil turtle _symtable fnmatch platform turtledemo _sysconfigdata_aarch64_conda_cos7_linux_gnu fontTools platformdirs typed_ast _sysconfigdata_i686_conda_cos6_linux_gnu formatter plistlib types _sysconfigdata_m_linux_x86_64-linux-gnu fractions pluggy typing _sysconfigdata_powerpc64le_conda_cos7_linux_gnu frozenlist poplib typing_extensions _sysconfigdata_x86_64_apple_darwin13_4_0 ftplib posix ufl _sysconfigdata_x86_64_conda_cos6_linux_gnu functools posixpath unicodedata _testbuffer gc pprint unittest _testcapi gem profile urllib _testimportmultiple genericpath prompt_toolkit urllib3 _testmultiphase genpy pstats uu _thread getopt psutil uuid _threading_local getpass pty venv _tkinter gettext ptyprocess versioneer _tracemalloc glob pulp vtk _warnings grp pvectorc vtkmodules _weakref gzip pwd warnings _weakrefset h5py py wave _xxtestfuzz hashlib py_compile wcwidth abc heapq pyadjoint weakref aifc hmac pybind11 webbrowser aiohttp html pyclbr wheel aiosignal http pycodestyle wrapt antigravity idlelib pycparser wsgiref appdirs idna pydoc wslink argparse imaplib pydoc_data xdist array imghdr pyexpat xdrlib ast imp pyflakes xml astroid importlib pygments xmlrpc async_timeout importlib_metadata pylab xxlimited asynchat importlib_resources pylint xxsubtype asyncio iniconfig pymbolic yarl asyncore inspect pyop2 zipapp asynctest io pyparsing zipfile atexit ipaddress pyrsistent zipimport attr ipykernel pytest zipp attrs ipykernel_launcher pytest_forked zlib audioop islpy pytools zmq autoreload isort pyximport backcall isympy queue Enter any module name to get more help. Or, type "modules spam" to search for modules whose name or summary contain the string "spam”. P.S.S. A simple “import * from firedrake” does not import python module, but only includes subdirectory firedrake……..I can import petsc4py, etc (as you can see it is an existing module). Firedrake does not exist?
participants (3)
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Ham, David A
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John Snyder
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Matthew Knepley