[petsc-users] How to read/write a HDF5 file using petsc4py ?
Quentin Chevalier
quentin.chevalier at polytechnique.edu
Fri Dec 10 03:02:32 CST 2021
Ok Matthew,
I'll list my steps :
*> sudo docker run -itv myfolder:/home/shared -w /home/shared/ --rm
dolfinx/dolfinxroot at container:/home/shared# echo $PETSCH_ARCH $PETSCH_DIR*
linux-gnu-real-32 /usr/local/petsc
*root at container:/home/shared# cd /usr/local/petsc*
*root at container:/usr/local/petsc# ./configure --with-hdf5 --with-petsc4py
--force*
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
The version of PETSc you are using is out-of-date, we recommend updating to
the new release
Available Version: 3.16.2 Installed Version: 3.16
https://petsc.org/release/download/
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
=============================================================================================
Configuring PETSc to compile on your system
=============================================================================================
TESTING: configureLibrary from
config.packages.petsc4py(config/BuildSystem/config/packages/petsc4py.py:116)
*******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for
details):
-------------------------------------------------------------------------------
PETSc4py requires Python with "cython" module(s) installed!
Please install using package managers - for ex: "apt" or "dnf" (on linux),
or with "pip" using: /usr/bin/python3 -m pip install cython
*******************************************************************************
*root at container:/usr/local/petsc# pip install cython*
Collecting cython
Downloading
Cython-0.29.25-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl
(1.9 MB)
|████████████████████████████████| 1.9 MB 10.8 MB/s
Installing collected packages: cython
Successfully installed cython-0.29.25
*root at container:/usr/local/petsc# ./configure --with-hdf5 --with-petsc4py
--force*
=============================================================================================
Configuring PETSc to compile on your system
=============================================================================================
Compilers:
C Compiler: mpicc -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -Wno-misleading-indentation
-Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g3 -O0
Version: gcc (Ubuntu 11.2.0-7ubuntu2) 11.2.0
C++ Compiler: mpicxx -Wall -Wwrite-strings -Wno-strict-aliasing
-Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g -O0 -fPIC
-std=gnu++17
Version: g++ (Ubuntu 11.2.0-7ubuntu2) 11.2.0
Fortran Compiler: mpif90 -fPIC -Wall -ffree-line-length-0
-Wno-unused-dummy-argument -g -O0
Version: GNU Fortran (Ubuntu 11.2.0-7ubuntu2) 11.2.0
Linkers:
Shared linker: mpicc -shared -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -Wno-misleading-indentation
-Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g3 -O0
Dynamic linker: mpicc -shared -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -Wno-misleading-indentation
-Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g3 -O0
Libraries linked against: -lquadmath -lstdc++ -ldl
BlasLapack:
Library: -llapack -lblas
Unknown if this uses OpenMP (try export OMP_NUM_THREADS=<1-4> yourprogram
-log_view)
uses 4 byte integers
MPI:
Version: 3
mpiexec: mpiexec
Implementation: mpich3
MPICH_NUMVERSION: 30402300
X:
Library: -lX11
pthread:
hdf5:
Version: 1.12.1
Library: -lhdf5_hl -lhdf5
cmake:
Version: 3.18.4
/usr/bin/cmake
regex:
Language used to compile PETSc: C
PETSc:
PETSC_ARCH: linux-gnu-real-32
PETSC_DIR: /usr/local/petsc
Prefix: <inplace installation>
Scalar type: real
Precision: double
Support for __float128
Integer size: 4 bytes
Single library: yes
Shared libraries: yes
Memory alignment from malloc(): 16 bytes
Using GNU make: /usr/bin/gmake
xxx=========================================================================xxx
Configure stage complete. Now build PETSc libraries with:
make PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-real-32 all
xxx=========================================================================xxx
*root at 17fbe5936a5d:/usr/local/petsc# make all*
/usr/bin/python3 ./config/gmakegen.py --petsc-arch=linux-gnu-real-32
/usr/bin/python3 /usr/local/petsc/config/gmakegentest.py
--petsc-dir=/usr/local/petsc --petsc-arch=linux-gnu-real-32
--testdir=./linux-gnu-real-32/tests
==========================================
See documentation/faq.html and documentation/bugreporting.html
for help with installation problems. Please send EVERYTHING
printed out below when reporting problems. Please check the
mailing list archives and consider subscribing.
https://petsc.org/release/community/mailing/
==========================================
Starting make run on 17fbe5936a5d at Fri, 10 Dec 2021 08:28:10 +0000
Machine characteristics: Linux 17fbe5936a5d 5.3.18d01-lp152.63-default #1
SMP PREEMPT Fri Feb 5 19:19:17 CET 2021 x86_64 x86_64 x86_64 GNU/Linux
-----------------------------------------
Using PETSc directory: /usr/local/petsc
Using PETSc arch: linux-gnu-real-32
-----------------------------------------
PETSC_VERSION_RELEASE 1
PETSC_VERSION_MAJOR 3
PETSC_VERSION_MINOR 16
PETSC_VERSION_SUBMINOR 0
PETSC_VERSION_PATCH 0
PETSC_VERSION_DATE "Sep 29, 2021"
PETSC_VERSION_GIT "v3.16.0"
PETSC_VERSION_DATE_GIT "2021-09-29 18:30:02 -0500"
PETSC_VERSION_EQ(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_ PETSC_VERSION_EQ
PETSC_VERSION_LT(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_LE(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_GT(MAJOR,MINOR,SUBMINOR) \
PETSC_VERSION_GE(MAJOR,MINOR,SUBMINOR) \
-----------------------------------------
Using configure Options: --with-hdf5 --with-petsc4py --force
Using configuration flags:
#define INCLUDED_PETSCCONF_H
#define PETSC_ARCH "linux-gnu-real-32"
#define PETSC_ATTRIBUTEALIGNED(size) __attribute((aligned(size)))
#define PETSC_Alignx(a,b)
#define PETSC_BLASLAPACK_UNDERSCORE 1
#define PETSC_CLANGUAGE_C 1
#define PETSC_CXX_INLINE inline
#define PETSC_CXX_RESTRICT __restrict
#define PETSC_C_INLINE inline
#define PETSC_C_RESTRICT __restrict
#define PETSC_DEPRECATED_ENUM(why) __attribute((deprecated))
#define PETSC_DEPRECATED_FUNCTION(why) __attribute((deprecated))
#define PETSC_DEPRECATED_MACRO(why) _Pragma(why)
#define PETSC_DEPRECATED_TYPEDEF(why) __attribute((deprecated))
#define PETSC_DIR "/usr/local/petsc"
#define PETSC_DIR_SEPARATOR '/'
#define PETSC_FORTRAN_CHARLEN_T size_t
#define PETSC_FORTRAN_TYPE_INITIALIZE = -2
#define PETSC_FUNCTION_NAME_C __func__
#define PETSC_FUNCTION_NAME_CXX __func__
#define PETSC_HAVE_ACCESS 1
#define PETSC_HAVE_ATOLL 1
#define PETSC_HAVE_ATTRIBUTEALIGNED 1
#define PETSC_HAVE_BUILTIN_EXPECT 1
#define PETSC_HAVE_BZERO 1
#define PETSC_HAVE_C99_COMPLEX 1
#define PETSC_HAVE_CLOCK 1
#define PETSC_HAVE_CXX 1
#define PETSC_HAVE_CXX_COMPLEX 1
#define PETSC_HAVE_CXX_COMPLEX_FIX 1
#define PETSC_HAVE_CXX_DIALECT_CXX03 1
#define PETSC_HAVE_CXX_DIALECT_CXX11 1
#define PETSC_HAVE_CXX_DIALECT_CXX14 1
#define PETSC_HAVE_CXX_DIALECT_CXX17 1
#define PETSC_HAVE_DLADDR 1
#define PETSC_HAVE_DLCLOSE 1
#define PETSC_HAVE_DLERROR 1
#define PETSC_HAVE_DLFCN_H 1
#define PETSC_HAVE_DLOPEN 1
#define PETSC_HAVE_DLSYM 1
#define PETSC_HAVE_DOUBLE_ALIGN_MALLOC 1
#define PETSC_HAVE_DRAND48 1
#define PETSC_HAVE_DYNAMIC_LIBRARIES 1
#define PETSC_HAVE_ERF 1
#define PETSC_HAVE_FCNTL_H 1
#define PETSC_HAVE_FENV_H 1
#define PETSC_HAVE_FLOAT_H 1
#define PETSC_HAVE_FORK 1
#define PETSC_HAVE_FORTRAN 1
#define PETSC_HAVE_FORTRAN_FLUSH 1
#define PETSC_HAVE_FORTRAN_GET_COMMAND_ARGUMENT 1
#define PETSC_HAVE_FORTRAN_TYPE_STAR 1
#define PETSC_HAVE_FORTRAN_UNDERSCORE 1
#define PETSC_HAVE_GETCWD 1
#define PETSC_HAVE_GETDOMAINNAME 1
#define PETSC_HAVE_GETHOSTBYNAME 1
#define PETSC_HAVE_GETHOSTNAME 1
#define PETSC_HAVE_GETPAGESIZE 1
#define PETSC_HAVE_GETRUSAGE 1
#define PETSC_HAVE_HDF5 1
#define PETSC_HAVE_IMMINTRIN_H 1
#define PETSC_HAVE_INTTYPES_H 1
#define PETSC_HAVE_ISINF 1
#define PETSC_HAVE_ISNAN 1
#define PETSC_HAVE_ISNORMAL 1
#define PETSC_HAVE_LGAMMA 1
#define PETSC_HAVE_LOG2 1
#define PETSC_HAVE_LSEEK 1
#define PETSC_HAVE_MALLOC_H 1
#define PETSC_HAVE_MEMALIGN 1
#define PETSC_HAVE_MEMMOVE 1
#define PETSC_HAVE_MMAP 1
#define PETSC_HAVE_MPICH_NUMVERSION 30402300
#define PETSC_HAVE_MPIEXEC_ENVIRONMENTAL_VARIABLE MPIR_CVAR_CH3
#define PETSC_HAVE_MPIIO 1
#define PETSC_HAVE_MPI_COMBINER_CONTIGUOUS 1
#define PETSC_HAVE_MPI_COMBINER_DUP 1
#define PETSC_HAVE_MPI_COMBINER_NAMED 1
#define PETSC_HAVE_MPI_EXSCAN 1
#define PETSC_HAVE_MPI_F90MODULE 1
#define PETSC_HAVE_MPI_F90MODULE_VISIBILITY 1
#define PETSC_HAVE_MPI_FEATURE_DYNAMIC_WINDOW 1
#define PETSC_HAVE_MPI_FINALIZED 1
#define PETSC_HAVE_MPI_GET_ACCUMULATE 1
#define PETSC_HAVE_MPI_GET_LIBRARY_VERSION 1
#define PETSC_HAVE_MPI_IALLREDUCE 1
#define PETSC_HAVE_MPI_IBARRIER 1
#define PETSC_HAVE_MPI_INIT_THREAD 1
#define PETSC_HAVE_MPI_INT64_T 1
#define PETSC_HAVE_MPI_IN_PLACE 1
#define PETSC_HAVE_MPI_LONG_DOUBLE 1
#define PETSC_HAVE_MPI_NEIGHBORHOOD_COLLECTIVES 1
#define PETSC_HAVE_MPI_NONBLOCKING_COLLECTIVES 1
#define PETSC_HAVE_MPI_ONE_SIDED 1
#define PETSC_HAVE_MPI_PROCESS_SHARED_MEMORY 1
#define PETSC_HAVE_MPI_REDUCE_LOCAL 1
#define PETSC_HAVE_MPI_REDUCE_SCATTER 1
#define PETSC_HAVE_MPI_REDUCE_SCATTER_BLOCK 1
#define PETSC_HAVE_MPI_RGET 1
#define PETSC_HAVE_MPI_TYPE_DUP 1
#define PETSC_HAVE_MPI_TYPE_GET_ENVELOPE 1
#define PETSC_HAVE_MPI_WIN_CREATE 1
#define PETSC_HAVE_NANOSLEEP 1
#define PETSC_HAVE_NETDB_H 1
#define PETSC_HAVE_NETINET_IN_H 1
#define PETSC_HAVE_PACKAGES
":blaslapack:hdf5:mathlib:mpi:pthread:regex:x11:"
#define PETSC_HAVE_PETSC4PY 1
#define PETSC_HAVE_POPEN 1
#define PETSC_HAVE_PTHREAD 1
#define PETSC_HAVE_PTHREAD_BARRIER_T 1
#define PETSC_HAVE_PTHREAD_H 1
#define PETSC_HAVE_PWD_H 1
#define PETSC_HAVE_RAND 1
#define PETSC_HAVE_READLINK 1
#define PETSC_HAVE_REALPATH 1
#define PETSC_HAVE_REAL___FLOAT128 1
#define PETSC_HAVE_REGEX 1
#define PETSC_HAVE_RTLD_GLOBAL 1
#define PETSC_HAVE_RTLD_LAZY 1
#define PETSC_HAVE_RTLD_LOCAL 1
#define PETSC_HAVE_RTLD_NOW 1
#define PETSC_HAVE_SCHED_CPU_SET_T 1
#define PETSC_HAVE_SETJMP_H 1
#define PETSC_HAVE_SLEEP 1
#define PETSC_HAVE_SNPRINTF 1
#define PETSC_HAVE_SOCKET 1
#define PETSC_HAVE_SO_REUSEADDR 1
#define PETSC_HAVE_STDINT_H 1
#define PETSC_HAVE_STRCASECMP 1
#define PETSC_HAVE_STRINGS_H 1
#define PETSC_HAVE_STRUCT_SIGACTION 1
#define PETSC_HAVE_SYSINFO 1
#define PETSC_HAVE_SYS_PARAM_H 1
#define PETSC_HAVE_SYS_PROCFS_H 1
#define PETSC_HAVE_SYS_RESOURCE_H 1
#define PETSC_HAVE_SYS_SOCKET_H 1
#define PETSC_HAVE_SYS_SYSINFO_H 1
#define PETSC_HAVE_SYS_TIMES_H 1
#define PETSC_HAVE_SYS_TIME_H 1
#define PETSC_HAVE_SYS_TYPES_H 1
#define PETSC_HAVE_SYS_UTSNAME_H 1
#define PETSC_HAVE_SYS_WAIT_H 1
#define PETSC_HAVE_TGAMMA 1
#define PETSC_HAVE_TIME 1
#define PETSC_HAVE_TIME_H 1
#define PETSC_HAVE_UNAME 1
#define PETSC_HAVE_UNISTD_H 1
#define PETSC_HAVE_USLEEP 1
#define PETSC_HAVE_VA_COPY 1
#define PETSC_HAVE_VSNPRINTF 1
#define PETSC_HAVE_X 1
#define PETSC_HAVE_XMMINTRIN_H 1
#define PETSC_HDF5_HAVE_PARALLEL 1
#define PETSC_HDF5_HAVE_ZLIB 1
#define PETSC_IS_COLORING_MAX USHRT_MAX
#define PETSC_IS_COLORING_VALUE_TYPE short
#define PETSC_IS_COLORING_VALUE_TYPE_F integer2
#define PETSC_LEVEL1_DCACHE_LINESIZE 64
#define PETSC_LIB_DIR "/usr/local/petsc/linux-gnu-real-32/lib"
#define PETSC_MAX_PATH_LEN 4096
#define PETSC_MEMALIGN 16
#define PETSC_MPICC_SHOW "gcc -I/usr/local/include -L/usr/local/lib
-Wl,-rpath -Wl,/usr/local/lib -Wl,--enable-new-dtags -lmpi"
#define PETSC_MPIU_IS_COLORING_VALUE_TYPE MPI_UNSIGNED_SHORT
#define PETSC_PETSC4PY_INSTALL_PATH "/usr/local/petsc/linux-gnu-real-32/lib"
#define PETSC_PREFETCH_HINT_NTA _MM_HINT_NTA
#define PETSC_PREFETCH_HINT_T0 _MM_HINT_T0
#define PETSC_PREFETCH_HINT_T1 _MM_HINT_T1
#define PETSC_PREFETCH_HINT_T2 _MM_HINT_T2
#define PETSC_PYTHON_EXE "/usr/bin/python3"
#define PETSC_Prefetch(a,b,c) _mm_prefetch((const char*)(a),(c))
#define PETSC_REPLACE_DIR_SEPARATOR '\\'
#define PETSC_SIGNAL_CAST
#define PETSC_SIZEOF_ENUM 4
#define PETSC_SIZEOF_INT 4
#define PETSC_SIZEOF_LONG 8
#define PETSC_SIZEOF_LONG_LONG 8
#define PETSC_SIZEOF_SHORT 2
#define PETSC_SIZEOF_SIZE_T 8
#define PETSC_SIZEOF_VOID_P 8
#define PETSC_SLSUFFIX "so"
#define PETSC_UINTPTR_T uintptr_t
#define PETSC_UNUSED __attribute((unused))
#define PETSC_USE_AVX512_KERNELS 1
#define PETSC_USE_BACKWARD_LOOP 1
#define PETSC_USE_CTABLE 1
#define PETSC_USE_DEBUG 1
#define PETSC_USE_DEBUGGER "gdb"
#define PETSC_USE_INFO 1
#define PETSC_USE_ISATTY 1
#define PETSC_USE_LOG 1
#define PETSC_USE_PROC_FOR_SIZE 1
#define PETSC_USE_REAL_DOUBLE 1
#define PETSC_USE_SHARED_LIBRARIES 1
#define PETSC_USE_SINGLE_LIBRARY 1
#define PETSC_USE_SOCKET_VIEWER 1
#define PETSC_USE_VISIBILITY_C 1
#define PETSC_USE_VISIBILITY_CXX 1
#define PETSC_USING_64BIT_PTR 1
#define PETSC_USING_F2003 1
#define PETSC_USING_F90FREEFORM 1
#define PETSC__BSD_SOURCE 1
#define PETSC__DEFAULT_SOURCE 1
#define PETSC__GNU_SOURCE 1
-----------------------------------------
Using C compile: mpicc -o .o -c -fPIC -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -Wno-misleading-indentation
-Wno-stringop-overflow -fstack-protector -fvisibility=hidden -g3 -O0
mpicc -show: gcc -I/usr/local/include -L/usr/local/lib -Wl,-rpath
-Wl,/usr/local/lib -Wl,--enable-new-dtags -lmpi
C compiler version: gcc (Ubuntu 11.2.0-7ubuntu2) 11.2.0
Using C++ compile: mpicxx -o .o -c -Wall -Wwrite-strings
-Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector
-fvisibility=hidden -g -O0 -fPIC -std=gnu++17 -I/usr/local/petsc/include
-I/usr/local/petsc/linux-gnu-real-32/include
mpicxx -show: g++ -I/usr/local/include -L/usr/local/lib -lmpicxx -Wl,-rpath
-Wl,/usr/local/lib -Wl,--enable-new-dtags -lmpi
C++ compiler version: g++ (Ubuntu 11.2.0-7ubuntu2) 11.2.0
Using Fortran compile: mpif90 -o .o -c -fPIC -Wall -ffree-line-length-0
-Wno-unused-dummy-argument -g -O0 -I/usr/local/petsc/include
-I/usr/local/petsc/linux-gnu-real-32/include
mpif90 -show: gfortran -I/usr/local/include -I/usr/local/include
-L/usr/local/lib -lmpifort -Wl,-rpath -Wl,/usr/local/lib
-Wl,--enable-new-dtags -lmpi
Fortran compiler version: GNU Fortran (Ubuntu 11.2.0-7ubuntu2) 11.2.0
-----------------------------------------
Using C/C++ linker: mpicc
Using C/C++ flags: -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing
-Wno-unknown-pragmas -Wno-misleading-indentation -Wno-stringop-overflow
-fstack-protector -fvisibility=hidden -g3 -O0
Using Fortran linker: mpif90
Using Fortran flags: -fPIC -Wall -ffree-line-length-0
-Wno-unused-dummy-argument -g -O0
-----------------------------------------
Using system modules:
Using mpi.h: # 1 "/usr/local/include/mpi.h" 1 3
-----------------------------------------
Using libraries: -Wl,-rpath,/usr/local/petsc/linux-gnu-real-32/lib
-L/usr/local/petsc/linux-gnu-real-32/lib -Wl,-rpath,/usr/local/lib
-L/usr/local/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/11
-L/usr/lib/gcc/x86_64-linux-gnu/11 -lpetsc -llapack -lblas -lhdf5_hl -lhdf5
-lm -lX11 -lstdc++ -ldl -lmpifort -lmpi -lgfortran -lm -lgfortran -lm
-lgcc_s -lquadmath -lstdc++ -ldl
------------------------------------------
Using mpiexec: mpiexec
------------------------------------------
Using MAKE: /usr/bin/gmake
Using MAKEFLAGS: -j10 -l18.0 --no-print-directory --
PETSC_DIR=/usr/local/petsc PETSC_ARCH=linux-gnu-real-32
==========================================
gmake[3]: Nothing to be done for 'libs'.
*** Building petsc4py ***
/usr/bin/bash: line 1: cd: src/binding/petsc4py: No such file or directory
**************************ERROR*************************************
Error building petsc4py.
********************************************************************
gmake[2]: ***
[/usr/local/petsc/linux-gnu-real-32/lib/petsc/conf/petscrules:45:
petsc4pybuild] Error 1
**************************ERROR*************************************
Error during compile, check linux-gnu-real-32/lib/petsc/conf/make.log
Send it and linux-gnu-real-32/lib/petsc/conf/configure.log to
petsc-maint at mcs.anl.gov
********************************************************************
gmake[1]: *** [makefile:40: all] Error 1
make: *** [GNUmakefile:9: all] Error 2
Sorry for the massive text blob, but that was definitely unexepcted
behaviour. I know I mailed before saying the --with-petsc4py option didn't
change a thing, but now it seems to be breaking everything. I serached a
bit through make.log and didn't find anything useful.
Quentin
[image: cid:image003.jpg at 01D690CB.3B3FDC10]
Quentin CHEVALIER – IA parcours recherche
LadHyX - Ecole polytechnique
__________
On Thu, 9 Dec 2021 at 18:02, Matthew Knepley <knepley at gmail.com> wrote:
> On Thu, Dec 9, 2021 at 11:40 AM Quentin Chevalier <
> quentin.chevalier at polytechnique.edu> wrote:
>
>> Hello Matthew,
>>
>> You're absolutely right ! Editor error, my apologies. Running full
>> process 1-5) in container gives :
>>
>> root at container_id: ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres
>> lid velocity = 0.0016, prandtl # = 1., grashof # = 1.
>> Number of SNES iterations = 2
>>
>> So I guess it is passing the test.
>
>
> Yes, that is right.
>
>
>> I guess it is a site-wide
>> installation then. Is that good news or bad news when it comes to
>> adding HDF5 on top of things ?
>>
>
> It is fine either way. You should now be able to get further. petsc4py
> should be just using the shared
> libraries, so you should now be able to run an HDF5 thing from there. Does
> it work?
>
> Thanks,
>
> Matt
>
>
>> Thank you for your time,
>>
>> Quentin
>>
>> On Wed, 8 Dec 2021 at 19:12, Matthew Knepley <knepley at gmail.com> wrote:
>> >
>> > On Wed, Dec 8, 2021 at 11:05 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >>
>> >> Sorry Matthew, I had a correct tabulation. The attached file gives the
>> >> same error.
>> >
>> >
>> > The file you attached has 6 spaces in front of ${CLINKER} rather than a
>> tab character.
>> >
>> > Thanks,
>> >
>> > Matt
>> >
>> >>
>> >> Quentin
>> >>
>> >>
>> >>
>> >> Quentin CHEVALIER – IA parcours recherche
>> >>
>> >> LadHyX - Ecole polytechnique
>> >>
>> >> __________
>> >>
>> >>
>> >>
>> >> On Wed, 8 Dec 2021 at 16:51, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >> >
>> >> > On Wed, Dec 8, 2021 at 9:39 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >>
>> >> >> Step 4) fails. Traceback is : makefile:2: *** missing separator.
>> Stop.
>> >> >
>> >> >
>> >> > Makefiles require a tab character at the beginning of every action
>> line. When you cut & pasted from email
>> >> > the tab got eaten. Once you put it back, the makefile will work.
>> >> >
>> >> >>
>> >> >> echo $CLINKER return an empty line. Same for PETSC_LIB. It would
>> seem
>> >> >> the docker container has no such environment variables. Or did you
>> >> >> expect me to replace these by an environment specific linker ?
>> >> >
>> >> >
>> >> > Those variables are defined in the included makefile
>> >> >
>> >> > include ${PETSC_DIR}/lib/petsc/conf/variables
>> >> >
>> >> > Thanks,
>> >> >
>> >> > Matt
>> >> >
>> >> >>
>> >> >> Quentin
>> >> >>
>> >> >>
>> >> >>
>> >> >> Quentin CHEVALIER – IA parcours recherche
>> >> >>
>> >> >> LadHyX - Ecole polytechnique
>> >> >>
>> >> >> __________
>> >> >>
>> >> >>
>> >> >>
>> >> >> On Wed, 8 Dec 2021 at 15:14, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >> >> >
>> >> >> > On Wed, Dec 8, 2021 at 9:07 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >>
>> >> >> >> I'm not sure I understand what you're saying... But it's my
>> theory
>> >> >> >> from the beginning that make check fails because PETSc examples
>> were
>> >> >> >> taken out of the docker image.
>> >> >> >
>> >> >> >
>> >> >> > It appears so. There is no 'src' directory. Here is a simple way
>> to test with an install like this.
>> >> >> >
>> >> >> > 1) mkdir test; cd test
>> >> >> >
>> >> >> > 2) Download the source:
>> https://gitlab.com/petsc/petsc/-/raw/main/src/snes/tutorials/ex19.c?inline=false
>> >> >> >
>> >> >> > 3) Create a simple makefile:
>> >> >> >
>> >> >> > ex19: ex19.o
>> >> >> > ${CLINKER} -o ex19 ex19.o ${PETSC_LIB}
>> >> >> >
>> >> >> > include ${PETSC_DIR}/lib/petsc/conf/variables
>> >> >> > include ${PETSC_DIR}/lib/petsc/conf/rules
>> >> >> >
>> >> >> > 4) make ex19
>> >> >> >
>> >> >> > 5) ./ex19 -da_refine 3 -pc_type mg -ksp_type fgmres
>> >> >> >
>> >> >> > Thanks,
>> >> >> >
>> >> >> > Matt
>> >> >> >
>> >> >> >> I'm unsure what would be the correct way to discriminate between
>> >> >> >> source and partial install, I tried a find . --name "testex19"
>> from
>> >> >> >> PETSC_DIR to no avail. A ls from PETSC_DIR yields :
>> CODE_OF_CONDUCT.md
>> >> >> >> CONTRIBUTING GNUmakefile LICENSE PKG-INFO config
>> configtest.mod
>> >> >> >> configure configure.log configure.log.bkp gmakefile
>> gmakefile.test
>> >> >> >> include interfaces lib linux-gnu-complex-32
>> linux-gnu-complex-64
>> >> >> >> linux-gnu-real-32 linux-gnu-real-64 make.log makefile
>> petscdir.mk
>> >> >> >> setup.py
>> >> >> >>
>> >> >> >> Quentin
>> >> >> >> On Wed, 8 Dec 2021 at 14:38, Matthew Knepley <knepley at gmail.com>
>> wrote:
>> >> >> >> >
>> >> >> >> > On Wed, Dec 8, 2021 at 8:29 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >>
>> >> >> >> >> @Matthew Knepley I'm confused by your comment. Judging from
>> the
>> >> >> >> >> traceback, PETSC_DIR is set and correct. You think it should
>> be
>> >> >> >> >> specified in the command line as well ?
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > You are right, usually this message
>> >> >> >> >
>> >> >> >> > >> /usr/bin/bash: line 1: cd: src/snes/tutorials: No such file
>> or directory
>> >> >> >> >
>> >> >> >> > means that PETSC_DIR is undefined, and thus you cannot find
>> the tutorials. However, it could be that
>> >> >> >> > Your PETSC_DIR refers to a site-wide installation, which
>> /usr/local/petsc seems like. There the source
>> >> >> >> > is not installed and we cannot run 'make check' because only
>> the headers and libraries are there. Is this
>> >> >> >> > what is happening here?
>> >> >> >> >
>> >> >> >> > Thanks,
>> >> >> >> >
>> >> >> >> > Matt
>> >> >> >> >
>> >> >> >> >>
>> >> >> >> >> Quentin
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> Quentin CHEVALIER – IA parcours recherche
>> >> >> >> >>
>> >> >> >> >> LadHyX - Ecole polytechnique
>> >> >> >> >>
>> >> >> >> >> __________
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Wed, 8 Dec 2021 at 13:23, Matthew Knepley <
>> knepley at gmail.com> wrote:
>> >> >> >> >> >
>> >> >> >> >> > On Wed, Dec 8, 2021 at 4:08 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> @all thanks for your time it's heartening to see a lively
>> community.
>> >> >> >> >> >>
>> >> >> >> >> >> @Barry I've restarted the container and grabbed the .log
>> file directly after the docker magic. I've tried a make check, it
>> unsurprisingly spews the same answer as before :
>> >> >> >> >> >>
>> >> >> >> >> >> Running check examples to verify correct installation
>> >> >> >> >> >> Using PETSC_DIR=/usr/local/petsc and
>> PETSC_ARCH=linux-gnu-real-32
>> >> >> >> >> >> /usr/bin/bash: line 1: cd: src/snes/tutorials: No such
>> file or directory
>> >> >> >> >> >> /usr/bin/bash: line 1: cd: src/snes/tutorials: No such
>> file or directory
>> >> >> >> >> >> gmake[3]: *** No rule to make target 'testex19'. Stop.
>> >> >> >> >> >> gmake[2]: *** [makefile:155: check_build] Error 2
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > This happens if you run 'make check' without defining
>> PETSC_DIR in your environment, since we are including
>> >> >> >> >> > makefiles with PETSC_DIR in the path and make does not
>> allow proper error messages in that case.
>> >> >> >> >> >
>> >> >> >> >> > Thanks,
>> >> >> >> >> >
>> >> >> >> >> > Matt
>> >> >> >> >> >
>> >> >> >> >> >>
>> >> >> >> >> >> @Matthew ok will do, but I think @Lawrence has already
>> provided that answer. It's possible to change the dockerfile and recompute
>> the dolfinx image with hdf5, only it is a time-consuming process.
>> >> >> >> >> >>
>> >> >> >> >> >> Quentin
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> Quentin CHEVALIER – IA parcours recherche
>> >> >> >> >> >>
>> >> >> >> >> >> LadHyX - Ecole polytechnique
>> >> >> >> >> >>
>> >> >> >> >> >> __________
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >>
>> >> >> >> >> >> On Tue, 7 Dec 2021 at 19:16, Matthew Knepley <
>> knepley at gmail.com> wrote:
>> >> >> >> >> >>>
>> >> >> >> >> >>> On Tue, Dec 7, 2021 at 9:43 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> @Matthew, as stated before, error output is unchanged,
>> i.e.the python
>> >> >> >> >> >>>> command below produces the same traceback :
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> # python3 -c "from petsc4py import PETSc;
>> PETSc.Viewer().createHDF5('d.h5')"
>> >> >> >> >> >>>> Traceback (most recent call last):
>> >> >> >> >> >>>> File "<string>", line 1, in <module>
>> >> >> >> >> >>>> File "PETSc/Viewer.pyx", line 182, in
>> petsc4py.PETSc.Viewer.createHDF5
>> >> >> >> >> >>>> petsc4py.PETSc.Error: error code 86
>> >> >> >> >> >>>> [0] PetscViewerSetType() at
>> >> >> >> >> >>>>
>> /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442
>> >> >> >> >> >>>> [0] Unknown type. Check for miss-spelling or missing
>> package:
>> >> >> >> >> >>>>
>> https://petsc.org/release/install/install/#external-packages
>> >> >> >> >> >>>> [0] Unknown PetscViewer type given: hdf5
>> >> >> >> >> >>>
>> >> >> >> >> >>>
>> >> >> >> >> >>> The reason I wanted the output was that the C output
>> shows the configure options that the PETSc library
>> >> >> >> >> >>> was built with, However, Python seems to be eating this,
>> so I cannot check.
>> >> >> >> >> >>>
>> >> >> >> >> >>> It seems like using this container is counter-productive.
>> If it was built correctly, making these changes would be trivial.
>> >> >> >> >> >>> Send mail to FEniCS (I am guessing Chris Richardson
>> maintains this), and ask how they intend people to change these
>> >> >> >> >> >>> options.
>> >> >> >> >> >>>
>> >> >> >> >> >>> Thanks,
>> >> >> >> >> >>>
>> >> >> >> >> >>> Matt.
>> >> >> >> >> >>>
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> @Wence that makes sense. I'd assumed that the original
>> PETSc had been
>> >> >> >> >> >>>> overwritten, and if the linking has gone wrong I'm
>> surprised anything
>> >> >> >> >> >>>> happens with petsc4py at all.
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> Your tentative command gave :
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> ERROR: Invalid requirement:
>> '/usr/local/petsc/src/binding/petsc4py'
>> >> >> >> >> >>>> Hint: It looks like a path. File
>> >> >> >> >> >>>> '/usr/local/petsc/src/binding/petsc4py' does not exist.
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> So I tested that global variables PETSC_ARCH & PETSC_DIR
>> were correct
>> >> >> >> >> >>>> then ran "pip install petsc4py" to restart petsc4py from
>> scratch. This
>> >> >> >> >> >>>> gives rise to a different error :
>> >> >> >> >> >>>> # python3 -c "from petsc4py import PETSc"
>> >> >> >> >> >>>> Traceback (most recent call last):
>> >> >> >> >> >>>> File "<string>", line 1, in <module>
>> >> >> >> >> >>>> File
>> "/usr/local/lib/python3.9/dist-packages/petsc4py/PETSc.py",
>> >> >> >> >> >>>> line 3, in <module>
>> >> >> >> >> >>>> PETSc = ImportPETSc(ARCH)
>> >> >> >> >> >>>> File
>> "/usr/local/lib/python3.9/dist-packages/petsc4py/lib/__init__.py",
>> >> >> >> >> >>>> line 29, in ImportPETSc
>> >> >> >> >> >>>> return Import('petsc4py', 'PETSc', path, arch)
>> >> >> >> >> >>>> File
>> "/usr/local/lib/python3.9/dist-packages/petsc4py/lib/__init__.py",
>> >> >> >> >> >>>> line 73, in Import
>> >> >> >> >> >>>> module = import_module(pkg, name, path, arch)
>> >> >> >> >> >>>> File
>> "/usr/local/lib/python3.9/dist-packages/petsc4py/lib/__init__.py",
>> >> >> >> >> >>>> line 58, in import_module
>> >> >> >> >> >>>> with f: return imp.load_module(fullname, f, fn, info)
>> >> >> >> >> >>>> File "/usr/lib/python3.9/imp.py", line 242, in
>> load_module
>> >> >> >> >> >>>> return load_dynamic(name, filename, file)
>> >> >> >> >> >>>> File "/usr/lib/python3.9/imp.py", line 342, in
>> load_dynamic
>> >> >> >> >> >>>> return _load(spec)
>> >> >> >> >> >>>> ImportError:
>> /usr/local/lib/python3.9/dist-packages/petsc4py/lib/linux-gnu-real-32/
>> PETSc.cpython-39-x86_64-linux-gnu.so:
>> >> >> >> >> >>>> undefined symbol: petscstack
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> Not sure that it a step forward ; looks like petsc4py is
>> broken now.
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> Quentin
>> >> >> >> >> >>>>
>> >> >> >> >> >>>> On Tue, 7 Dec 2021 at 14:58, Matthew Knepley <
>> knepley at gmail.com> wrote:
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> > On Tue, Dec 7, 2021 at 8:26 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> Ok my bad, that log corresponded to a tentative
>> --download-hdf5. This
>> >> >> >> >> >>>> >> log corresponds to the commands given above and has
>> --with-hdf5 in its
>> >> >> >> >> >>>> >> options.
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> > Okay, this configure was successful and found HDF5
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> The whole process still results in the same error.
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> > Now send me the complete error output with this PETSc.
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> > Thanks,
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> > Matt
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> Quentin
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> Quentin CHEVALIER – IA parcours recherche
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> LadHyX - Ecole polytechnique
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> __________
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >>
>> >> >> >> >> >>>> >> On Tue, 7 Dec 2021 at 13:59, Matthew Knepley <
>> knepley at gmail.com> wrote:
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > On Tue, Dec 7, 2021 at 3:55 AM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> Hello Matthew,
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> That would indeed make sense.
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> Full log is attached, I grepped hdf5 in there and
>> didn't find anything alarming.
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > At the top of this log:
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > Configure Options: --configModules=PETSc.Configure
>> --optionsModule=config.compilerOptions PETSC_ARCH=linux-gnu-complex-64
>> --COPTFLAGS=-O2 --CXXOPTFLAGS=-O2 --FOPTFLAGS=-O2 --with-make-np=2
>> --with-64-bit-indices=yes --with-debugging=no --with-fortran-bindings=no
>> --with-shared-libraries --download-hypre --download-mumps
>> --download-ptscotch --download-scalapack --download-suitesparse
>> --download-superlu_dist --with-scalar-type=complex
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > So the HDF5 option is not being specified.
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > Thanks,
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > Matt
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> >> Cheers,
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> Quentin
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> Quentin CHEVALIER – IA parcours recherche
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> LadHyX - Ecole polytechnique
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> __________
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >>
>> >> >> >> >> >>>> >> >> On Mon, 6 Dec 2021 at 21:39, Matthew Knepley <
>> knepley at gmail.com> wrote:
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> On Mon, Dec 6, 2021 at 3:27 PM Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>> Fine. MWE is unchanged :
>> >> >> >> >> >>>> >> >>>> * Run this docker container
>> >> >> >> >> >>>> >> >>>> * Do : python3 -c "from petsc4py import PETSc;
>> PETSc.Viewer().createHDF5('dummy.h5')"
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>> Updated attempt at a fix :
>> >> >> >> >> >>>> >> >>>> * cd /usr/local/petsc/
>> >> >> >> >> >>>> >> >>>> * ./configure PETSC_ARCH= linux-gnu-real-32
>> PETSC_DIR=/usr/local/petsc --with-hdf5 --force
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> Did it find HDF5? If not, it will shut it off.
>> You need to send us
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> $PETSC_DIR/configure.log
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> so we can see what happened in the configure run.
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> Thanks,
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> Matt
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>> * make PETSC_DIR=/usr/local/petsc PETSC-ARCH=
>> linux-gnu-real-32 all
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>> Still no joy. The same error remains.
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>> Quentin
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>>
>> >> >> >> >> >>>> >> >>>> On Mon, 6 Dec 2021 at 20:04, Pierre Jolivet <
>> pierre at joliv.et> wrote:
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > On 6 Dec 2021, at 7:42 PM, Quentin Chevalier <
>> quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > The PETSC_DIR exactly corresponds to the
>> previous one, so I guess that rules option b) out, except if a specific
>> option is required to overwrite a previous installation of PETSc. As for
>> a), well I thought reconfiguring pretty direct, you're welcome to give me a
>> hint as to what could be wrong in the following process.
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > Steps to reproduce this behaviour are as
>> follows :
>> >> >> >> >> >>>> >> >>>> > * Run this docker container
>> >> >> >> >> >>>> >> >>>> > * Do : python3 -c "from petsc4py import PETSc;
>> PETSc.Viewer().createHDF5('dummy.h5')"
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > After you get the error Unknown PetscViewer
>> type, feel free to try :
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > * cd /usr/local/petsc/
>> >> >> >> >> >>>> >> >>>> > * ./configure --with-hfd5
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > It’s hdf5, not hfd5.
>> >> >> >> >> >>>> >> >>>> > It’s PETSC_ARCH, not PETSC-ARCH.
>> >> >> >> >> >>>> >> >>>> > PETSC_ARCH is missing from your configure line.
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > Thanks,
>> >> >> >> >> >>>> >> >>>> > Pierre
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > * make PETSC_DIR=/usr/local/petsc
>> PETSC-ARCH=linux-gnu-real-32 all
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > Then repeat the MWE and observe absolutely no
>> behavioural change whatsoever. I'm afraid I don't know PETSc well enough to
>> be surprised by that.
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > Quentin
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > Quentin CHEVALIER – IA parcours recherche
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > LadHyX - Ecole polytechnique
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > __________
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > On Mon, 6 Dec 2021 at 19:24, Matthew Knepley <
>> knepley at gmail.com> wrote:
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> On Mon, Dec 6, 2021 at 1:22 PM Quentin
>> Chevalier <quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> It failed all of the tests included in `make
>> >> >> >> >> >>>> >> >>>> >>> PETSC_DIR=/usr/local/petsc
>> PETSC-ARCH=linux-gnu-real-32 check`, with
>> >> >> >> >> >>>> >> >>>> >>> the error `/usr/bin/bash: line 1: cd:
>> src/snes/tutorials: No such file
>> >> >> >> >> >>>> >> >>>> >>> or directory`
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> I am therefore fairly confident this a "file
>> absence" problem, and not
>> >> >> >> >> >>>> >> >>>> >>> a compilation problem.
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> I repeat that there was no error at
>> compilation stage. The final stage
>> >> >> >> >> >>>> >> >>>> >>> did present `gmake[3]: Nothing to be done
>> for 'libs'.` but that's all.
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> Again, running `./configure --with-hdf5`
>> followed by a `make
>> >> >> >> >> >>>> >> >>>> >>> PETSC_DIR=/usr/local/petsc
>> PETSC-ARCH=linux-gnu-real-32 all` does not
>> >> >> >> >> >>>> >> >>>> >>> change the problem. I get the same error at
>> the same position as
>> >> >> >> >> >>>> >> >>>> >>> before.
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> If you reconfigured and rebuilt, it is
>> impossible to get the same error, so
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> a) You did not reconfigure
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> b) Your new build is somewhere else on the
>> machine
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> Thanks,
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> Matt
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> I will comment I am running on OpenSUSE.
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> Quentin
>> >> >> >> >> >>>> >> >>>> >>>
>> >> >> >> >> >>>> >> >>>> >>> On Mon, 6 Dec 2021 at 19:09, Matthew Knepley
>> <knepley at gmail.com> wrote:
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> > On Mon, Dec 6, 2021 at 1:08 PM Quentin
>> Chevalier <quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> Hello Matthew and thanks for your quick
>> response.
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> I'm afraid I did try to snoop around the
>> container and rerun PETSc's
>> >> >> >> >> >>>> >> >>>> >>> >> configure with the --with-hdf5 option, to
>> absolutely no avail.
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> I didn't see any errors during config or
>> make, but it failed the tests
>> >> >> >> >> >>>> >> >>>> >>> >> (which aren't included in the minimal
>> container I suppose)
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> > Failed which tests? What was the error?
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> > Thanks,
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> > Matt
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> Quentin
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> Quentin CHEVALIER – IA parcours recherche
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> LadHyX - Ecole polytechnique
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> __________
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >>
>> >> >> >> >> >>>> >> >>>> >>> >> On Mon, 6 Dec 2021 at 19:02, Matthew
>> Knepley <knepley at gmail.com> wrote:
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> > On Mon, Dec 6, 2021 at 11:28 AM Quentin
>> Chevalier <quentin.chevalier at polytechnique.edu> wrote:
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> Hello PETSc users,
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> This email is a duplicata of this
>> gitlab issue, sorry for any inconvenience caused.
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> I want to compute a PETSc vector in
>> real mode, than perform calculations with it in complex mode. I want as
>> much of this process to be parallel as possible. Right now, I compile PETSc
>> in real mode, compute my vector and save it to a file, then switch to
>> complex mode, read it, and move on.
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> This creates unexpected behaviour
>> using MPIIO, so on Lisandro Dalcinl's advice I'm moving to HDF5 format. My
>> code is as follows (taking inspiration from petsc4py doc, a bitbucket
>> example and another one, all top Google results for 'petsc hdf5') :
>> >> >> >> >> >>>> >> >>>> >>> >> >>>
>> >> >> >> >> >>>> >> >>>> >>> >> >>> viewer =
>> PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)
>> >> >> >> >> >>>> >> >>>> >>> >> >>> q.load(viewer)
>> >> >> >> >> >>>> >> >>>> >>> >> >>>
>> q.ghostUpdate(addv=PETSc.InsertMode.INSERT, mode=PETSc.ScatterMode.FORWARD)
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> This crashes my code. I obtain
>> traceback :
>> >> >> >> >> >>>> >> >>>> >>> >> >>>
>> >> >> >> >> >>>> >> >>>> >>> >> >>> File "/home/shared/code.py", line
>> 121, in Load
>> >> >> >> >> >>>> >> >>>> >>> >> >>> viewer =
>> PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)
>> >> >> >> >> >>>> >> >>>> >>> >> >>> File "PETSc/Viewer.pyx", line 182,
>> in petsc4py.PETSc.Viewer.createHDF5
>> >> >> >> >> >>>> >> >>>> >>> >> >>> petsc4py.PETSc.Error: error code 86
>> >> >> >> >> >>>> >> >>>> >>> >> >>> [0] PetscViewerSetType() at
>> /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442
>> >> >> >> >> >>>> >> >>>> >>> >> >>> [0] Unknown type. Check for
>> miss-spelling or missing package:
>> https://petsc.org/release/install/install/#external-packages
>> >> >> >> >> >>>> >> >>>> >>> >> >>> [0] Unknown PetscViewer type given:
>> hdf5
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> > This means that PETSc has not been
>> configured with HDF5 (--with-hdf5 or --download-hdf5), so the container
>> should be updated.
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> > THanks,
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> > Matt
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> I have petsc4py 3.16 from this docker
>> container (list of dependencies include PETSc and petsc4py).
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> I'm pretty sure this is not intended
>> behaviour. Any insight as to how to fix this issue (I tried running
>> ./configure --with-hdf5 to no avail) or more generally to perform this
>> jiggling between real and complex would be much appreciated,
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> Kind regards.
>> >> >> >> >> >>>> >> >>>> >>> >> >>
>> >> >> >> >> >>>> >> >>>> >>> >> >> Quentin
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> >
>> >> >> >> >> >>>> >> >>>> >>> >> > --
>> >> >> >> >> >>>> >> >>>> >>> >> > 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/
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> >
>> >> >> >> >> >>>> >> >>>> >>> > --
>> >> >> >> >> >>>> >> >>>> >>> > 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/
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >>
>> >> >> >> >> >>>> >> >>>> >> --
>> >> >> >> >> >>>> >> >>>> >> 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/
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> > <image003.jpg>
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>> >
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>>
>> >> >> >> >> >>>> >> >>> --
>> >> >> >> >> >>>> >> >>> 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/
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> >
>> >> >> >> >> >>>> >> > --
>> >> >> >> >> >>>> >> > 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/
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> >
>> >> >> >> >> >>>> > --
>> >> >> >> >> >>>> > 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/
>> >> >> >> >> >>>
>> >> >> >> >> >>>
>> >> >> >> >> >>>
>> >> >> >> >> >>> --
>> >> >> >> >> >>> 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/
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > 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/
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > 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/
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > 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/
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > 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/
>> >
>> >
>> >
>> > --
>> > 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/
>>
>
>
> --
> 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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