Paquets pour tirfm-deepfinder

marchand · August 8, 2024, 12:28pm

Bonjour,

Pour tourner un code utilisant TensorFlow, je voudrais savoir si les paquets suivants sont disponibles sur les noeuds GPU : dpkg-dev build-essential python3-dev freeglut3-dev freeglut3-dev libglu1-mesa-dev libgstreamer-plugins-base1.0-dev libgtk-3-dev libjpeg-dev libnotify-dev libpng-dev libsdl2-dev libsm-dev libtiff-dev libxtst-dev libwebkit2gtk-4.0-dev

Le code en question est GitHub - deep-finder/tirfm-deepfinder: This version of DeepFinder has been customized for detecting exocytosis events in TIRF microscopy.

Bien cordialement,

Joel Marchand

rey · August 9, 2024, 9:26pm

Bonjour @marchand

Non, il est nécessaire de créer un environnement conda ou une image singularity.

Cordialement.

marchand · August 11, 2024, 3:38pm

Bonjour,

Merci pour la réponse.

On ne dispose pas non plus de gcc & cie, cad d’outils pour compiler ? C’est voulu ?

Bien cordialement,

rey · August 11, 2024, 6:50pm

Bonjour,

Des compilers sont présents dans les environnements ad hoc (voir avec les commandes module avail, module load).

Cordialement.

marchand · August 12, 2024, 6:43am

Bonjour,
Merci !
J’ai pu avancer sur la compilation de Python 3.10.4, mais cela coince sur ce qui suit.
Une idée ?
Bien cordialement,
Joel

Rebuilding with profile guided optimizations:
rm -f profile-clean-stamp
make build_all CFLAGS_NODIST=" -fprofile-use -fprofile-correction" LDFLAGS_NODIST=“”
make[1]: Entering directory ‘/shared/home/marchand/Python-3.10.4’
CC=‘gcc -pthread’ LDSHARED=‘gcc -pthread -shared -fno-semantic-interposition ’ OPT=’-DNDEBUG -g -fwrapv -O3 -Wall’ _TCLTK_INCLUDES=‘-I/opt/conda/include’ _TCLTK_LIBS=‘-L/opt/conda/lib -ltk8.6 -ltkstub8.6 -ltcl8.6 -ltclstub8.6’ ./python -E ./setup.py build
running build
running build_ext
building ‘_dbm’ extension
gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-use -fprofile-correction -I./Include/internal -DHAVE_NDBM_H -I./Include -I/shared/home/marchand/python-3.10.4/include -I. -I/usr/local/include -I/shared/home/marchand/Python-3.10.4/Include -I/shared/home/marchand/Python-3.10.4 -c /shared/home/marchand/Python-3.10.4/Modules/_dbmmodule.c -o build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/_dbmmodule.o
/shared/home/marchand/Python-3.10.4/Modules/_dbmmodule.c:16:10: fatal error: ndbm.h: No such file or directory
16 | #include <ndbm.h>
| ^~~~~~~~
compilation terminated.
building ‘_gdbm’ extension
gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-use -fprofile-correction -I./Include/internal -I./Include -I/shared/home/marchand/python-3.10.4/include -I. -I/usr/local/include -I/shared/home/marchand/Python-3.10.4/Include -I/shared/home/marchand/Python-3.10.4 -c /shared/home/marchand/Python-3.10.4/Modules/_gdbmmodule.c -o build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/_gdbmmodule.o
/shared/home/marchand/Python-3.10.4/Modules/_gdbmmodule.c:12:10: fatal error: gdbm.h: No such file or directory
12 | #include “gdbm.h”
| ^~~~~~~~
compilation terminated.
building ‘zlib’ extension
gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-use -fprofile-correction -I./Include/internal -I./Include -I/shared/home/marchand/python-3.10.4/include -I. -I/usr/local/include -I/shared/home/marchand/Python-3.10.4/Include -I/shared/home/marchand/Python-3.10.4 -c /shared/home/marchand/Python-3.10.4/Modules/zlibmodule.c -o build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/zlibmodule.o
/shared/home/marchand/Python-3.10.4/Modules/zlibmodule.c: In function ‘zlib_adler32_impl.isra.0’:
/shared/home/marchand/Python-3.10.4/Modules/zlibmodule.c:1653:1: warning: ‘/shared/home/marchand/Python-3.10.4/build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/zlibmodule.gcda’ profile count data file not found [-Wmissing-profile]
1653 | }
| ^
gcc -pthread -shared -fno-semantic-interposition build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/zlibmodule.o -L/shared/home/marchand/python-3.10.4/lib -L/usr/local/lib -lz -o build/lib.linux-x86_64-3.10/zlib.cpython-310-x86_64-linux-gnu.so
/shared/software/conda/envs/gcc-9.3.0/bin/…/lib/gcc/x86_64-conda-linux-gnu/9.3.0/…/…/…/…/x86_64-conda-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
building ‘binascii’ extension
gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-use -fprofile-correction -I./Include/internal -I./Include -I/shared/home/marchand/python-3.10.4/include -I. -I/usr/local/include -I/shared/home/marchand/Python-3.10.4/Include -I/shared/home/marchand/Python-3.10.4 -c /shared/home/marchand/Python-3.10.4/Modules/binascii.c -o build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/binascii.o -DUSE_ZLIB_CRC32
/shared/home/marchand/Python-3.10.4/Modules/binascii.c: In function ‘binascii_a2b_hqx_impl.isra.0’:
/shared/home/marchand/Python-3.10.4/Modules/binascii.c:1690:1: warning: ‘/shared/home/marchand/Python-3.10.4/build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/binascii.gcda’ profile count data file not found [-Wmissing-profile]
1690 | }
| ^
gcc -pthread -shared -fno-semantic-interposition build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/binascii.o -L/shared/home/marchand/python-3.10.4/lib -L/usr/local/lib -lz -o build/lib.linux-x86_64-3.10/binascii.cpython-310-x86_64-linux-gnu.so
/shared/software/conda/envs/gcc-9.3.0/bin/…/lib/gcc/x86_64-conda-linux-gnu/9.3.0/…/…/…/…/x86_64-conda-linux-gnu/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
building ‘_uuid’ extension
gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-use -fprofile-correction -I./Include/internal -I./Include -I/shared/home/marchand/python-3.10.4/include -I. -I/usr/local/include -I/shared/home/marchand/Python-3.10.4/Include -I/shared/home/marchand/Python-3.10.4 -c /shared/home/marchand/Python-3.10.4/Modules/_uuidmodule.c -o build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/_uuidmodule.o
/shared/home/marchand/Python-3.10.4/Modules/_uuidmodule.c: In function ‘PyInit__uuid’:
/shared/home/marchand/Python-3.10.4/Modules/_uuidmodule.c:122:1: warning: ‘/shared/home/marchand/Python-3.10.4/build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/_uuidmodule.gcda’ profile count data file not found [-Wmissing-profile]
122 | }
| ^
gcc -pthread -shared -fno-semantic-interposition build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/_uuidmodule.o -L/shared/home/marchand/python-3.10.4/lib -L/usr/local/lib -o build/lib.linux-x86_64-3.10/_uuid.cpython-310-x86_64-linux-gnu.so
building ‘_ctypes’ extension
gcc -pthread -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fno-semantic-interposition -std=c99 -Wextra -Wno-unused-result -Wno-unused-parameter -Wno-missing-field-initializers -Werror=implicit-function-declaration -fvisibility=hidden -fprofile-use -fprofile-correction -I./Include/internal -I./Include -I/shared/home/marchand/python-3.10.4/include -I. -I/usr/local/include -I/shared/home/marchand/Python-3.10.4/Include -I/shared/home/marchand/Python-3.10.4 -c /shared/home/marchand/Python-3.10.4/Modules/_ctypes/_ctypes.c -o build/temp.linux-x86_64-3.10/shared/home/marchand/Python-3.10.4/Modules/_ctypes/_ctypes.o -DPy_BUILD_CORE_MODULE
/shared/home/marchand/Python-3.10.4/Modules/_ctypes/_ctypes.c:107:10: fatal error: ffi.h: No such file or directory
107 | #include <ffi.h>
| ^~~~~~~
compilation terminated.
*** WARNING: renaming “_uuid” since importing it failed: /shared/home/marchand/Python-3.10.4/build/lib.linux-x86_64-3.10/_uuid.cpython-310-x86_64-linux-gnu.so: undefined symbol: uuid_generate_time_safe

Python build finished successfully!
The necessary bits to build these optional modules were not found:
_bz2 _curses _curses_panel
_lzma _sqlite3 readline
To find the necessary bits, look in setup.py in detect_modules() for the module’s name.

The following modules found by detect_modules() in setup.py, have been
built by the Makefile instead, as configured by the Setup files:
_abc pwd time

Failed to build these modules:
_ctypes _dbm _gdbm
binascii zlib

Following modules built successfully but were removed because they could not be imported:
_uuid

running build_scripts
copying and adjusting /shared/home/marchand/Python-3.10.4/Tools/scripts/pydoc3 → build/scripts-3.10
copying and adjusting /shared/home/marchand/Python-3.10.4/Tools/scripts/idle3 → build/scripts-3.10
copying and adjusting /shared/home/marchand/Python-3.10.4/Tools/scripts/2to3 → build/scripts-3.10
changing mode of build/scripts-3.10/pydoc3 from 640 to 755
changing mode of build/scripts-3.10/idle3 from 640 to 755
changing mode of build/scripts-3.10/2to3 from 640 to 755
renaming build/scripts-3.10/pydoc3 to build/scripts-3.10/pydoc3.10
renaming build/scripts-3.10/idle3 to build/scripts-3.10/idle3.10
renaming build/scripts-3.10/2to3 to build/scripts-3.10/2to3-3.10
make[1]: Leaving directory ‘/shared/home/marchand/Python-3.10.4’

rey · August 12, 2024, 10:34am

Bonjour @marchand

Plus simple de procéder comme suit je pense:

eval "$(/opt/conda/bin/conda shell.bash hook)"
conda create -n toto python==3.10.4
conda activate toto

Cordialement.