Hi, I have been trying to build yt on Legion cluster at University College London. My default modules are... Currently Loaded Modulefiles: 1) shared 5) infinipath/base/2.1 9) nedit/5.6 2) intel/fce/10.1.008 6) infinipath/mpi/intel/2.1 10) mrxvt/0.5.4 3) intel/cce/10.1.008 7) torque/2.2.1 11) hdf5/1.6.6 4) intel/mkl/64emt/10.0.2.018 8) moab/5.3.0 I did a module purge. And added gcc module... Currently Loaded Modulefiles: 1) GCC/4.4.1 But, the install_script.sh crashes when building matplot with the following warning in the yt_install.log... gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -DPY_ARRAY_UNIQUE_SYMBOL=MPL_ARRAY_API -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/core/include -I/usr/local/include -I/usr/include -I. -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib/python2.6/site-packages/numpy/core/include -Isrc -Iagg24/include -I. -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/include/python2.6 -c src/path.cpp -o build/temp.linux-x86_64-2.6/src/path.o cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ In file included from /shared/ucl/test/GCC4/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/../../../../include/c++/4.4.1/ext/hash_map:59, from ./CXX/Extensions.hxx:68, from src/path.cpp:8: /shared/ucl/test/GCC4/lib/gcc/x86_64-unknown-linux-gnu/4.4.1/../../../../include/c++/4.4.1/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. Please let me know what could be happening here. Shankar
Hi Shankar,
Frankly, it looks like you did everything right. The fact that it dies with a warning is confusing to me, because those should be non-fatal. If possible, could you include a bit more of the output? Say, the last fifty or so lines? There might be something buried in there. (C++ is not known for making it easy to find the compilation failure point!) You might also try, just to be safe, setting CXXFLAGS and CFLAGS to include "-Wno-deprecated" inside the script, which should get rid of that warning. Thanks, Matt
Hi Matt, Below is a longish output from yt_install.log : gcc -std=c99 -Wno-long-long -O -fomit-frame-pointer -finline-functions -I. -I. -I../src -I../src -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c tselect.c -fPIC -DPIC -o .libs/tselect.lo tselect.c: In function `test_select_point': tselect.c:426: warning: passing arg 4 of `H5Sselect_elements' from incompatible pointer type Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /cvos/shared/apps/intel/mkl/10.0.2.018/lib/em64t/ libraries mkl,vml,guide not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /cvos/shared/apps/intel/mkl/10.0.2.018/lib/em64t/ libraries mkl,vml,guide not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib libraries lapack_atlas not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib building extension "numpy.core._sort" sources Generating build/src.linux-x86_64-2.6/numpy/core/include/numpy/config.h customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/include/python2.6 -c' gcc: _configtest.c gcc -pthread _configtest.o -o _configtest _configtest.o(.text+0xd): In function `main': /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/src/numpy-1.3.0/_configtest.c:5: undefined reference to `exp' collect2: ld returned 1 exit status _configtest.o(.text+0xd): In function `main': /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/src/numpy-1.3.0/_configtest.c:5: undefined reference to `exp' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/include/python2.6 -c' gcc: _configtest.c _configtest.c:1: warning: conflicting types for built-in function 'asin' _configtest.c:2: warning: conflicting types for built-in function 'cos' BUILDING MATPLOTLIB matplotlib: 0.99.1.1 python: 2.6.3 (r263:75183, Aug 19 2010, 20:38:01) [GCC 3.4.6 20060404 (Red Hat 3.4.6-11)] platform: linux2 REQUIRED DEPENDENCIES numpy: 1.3.0 freetype2: 9.7.3 OPTIONAL BACKEND DEPENDENCIES libpng: found, but unknown version (no pkg-config) * Could not find 'libpng' headers in any of * '/usr/local/include', '/usr/include', '.' Tkinter: Tkinter: 73770, Tk: 8.4, Tcl: 8.4 /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc lib/matplotlib/delaunay/_delaunay.cpp: In function `PyObject* compute_planes_method(PyObject*, PyObject*)': lib/matplotlib/delaunay/_delaunay.cpp:315: warning: 'y' might be used uninitialized in this function cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ src/backend_agg.cpp:3:17: png.h: No such file or directory error: command 'gcc' failed with exit status 1 The last error seems to be the culprit?. -shankar
Hi Shankar,
Ah, yes! Bingo. Okay, fortunately it looks like at some point in the past I added libpng to the install script options. If you edit install_script.sh and turn on INST_PNG, when you re-run I think it will give a shot at installing libpng independently of the OS. I believe that'll fix the issue, but let me know how it goes? Thanks, Matt
Hi Matt, I may be having pre-yt1.7 scripts. So I tried the following 3 ways but they are all failing. 1. I svn'd a copy of enzo ... Checked out external at revision 1808. Checked out revision 3068. but the install_script.sh that comes with it does not have INST_PNG. 2. So I tried getting YT in my home directory independent of enzo like... [ucapsag@login03 ~]$ svn export http://svn.enzotools.org/yt/branches/yt-1.7/doc/install_script.sh svn: REPORT request failed on '/yt/!svn/vcc/default' svn: Cannot replace a directory from within 3. Finally, I got hold of http://bitbucket.org/MatthewTurk/yt/src/8190256cc360/doc/install_script.sh and put it in my enzo's yt (of step 1 above). It hangs saying... running install_egg_info Writing /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//lib/python2.6/lib-dynload/Python-2.6.3-py2.6.egg-info if test -f /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python -o -h /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python; \ then rm -f /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python; \ else true; \ fi (cd /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin; ln python2.6 python) rm -f /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python-config (cd /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin; ln -s python2.6-config python-config) Creating directory /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//share/man/man1 /usr/bin/install -c -m 644 ./Misc/python.man \ /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//share/man/man1/python.1 /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/bin/python2.6: can't open file '/home/ucapsag/enzo3/src/yt/distribute_setup.py': [Errno 2] No such file or directory shankar
Hi Shankar,
Youch! Okay, so here's my suggestion. The error with 1.7 seems to be that it won't replace an existing file. Just cd into your home directory, and do this: svn export http://svn.enzotools.org/yt/trunk/doc/install_script.sh Then, make sure there're no yt-i386 or yt-x86_64 directories or anything in your home directory. Then edit the script, set INST_PNG=1, and run: bash install_script.sh This should be totally clean. I'm going to try to disable the yt install script inside enzo, because we're moving away from that model of distribution. Anyway, let me know how that goes. Sorry this is so troublesome! -Matt
Hi Shankar,
Frankly, it looks like you did everything right. The fact that it dies with a warning is confusing to me, because those should be non-fatal. If possible, could you include a bit more of the output? Say, the last fifty or so lines? There might be something buried in there. (C++ is not known for making it easy to find the compilation failure point!) You might also try, just to be safe, setting CXXFLAGS and CFLAGS to include "-Wno-deprecated" inside the script, which should get rid of that warning. Thanks, Matt
Hi Matt, Below is a longish output from yt_install.log : gcc -std=c99 -Wno-long-long -O -fomit-frame-pointer -finline-functions -I. -I. -I../src -I../src -UH5_DEBUG_API -DNDEBUG -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -D_POSIX_SOURCE -D_BSD_SOURCE -c tselect.c -fPIC -DPIC -o .libs/tselect.lo tselect.c: In function `test_select_point': tselect.c:426: warning: passing arg 4 of `H5Sselect_elements' from incompatible pointer type Running from numpy source directory. non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2 blas_opt_info: blas_mkl_info: libraries mkl,vml,guide not found in /cvos/shared/apps/intel/mkl/10.0.2.018/lib/em64t/ libraries mkl,vml,guide not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE lapack_mkl_info: mkl_info: libraries mkl,vml,guide not found in /cvos/shared/apps/intel/mkl/10.0.2.018/lib/em64t/ libraries mkl,vml,guide not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib libraries mkl,vml,guide not found in /usr/local/lib64 libraries mkl,vml,guide not found in /usr/local/lib libraries mkl,vml,guide not found in /usr/lib64 libraries mkl,vml,guide not found in /usr/lib NOT AVAILABLE NOT AVAILABLE atlas_threads_info: Setting PTATLAS=ATLAS libraries ptf77blas,ptcblas,atlas not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib libraries lapack_atlas not found in /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/lib building extension "numpy.core._sort" sources Generating build/src.linux-x86_64-2.6/numpy/core/include/numpy/config.h customize GnuFCompiler Found executable /usr/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize GnuFCompiler gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found C compiler: gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/include/python2.6 -c' gcc: _configtest.c gcc -pthread _configtest.o -o _configtest _configtest.o(.text+0xd): In function `main': /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/src/numpy-1.3.0/_configtest.c:5: undefined reference to `exp' collect2: ld returned 1 exit status _configtest.o(.text+0xd): In function `main': /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/src/numpy-1.3.0/_configtest.c:5: undefined reference to `exp' collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o compile options: '-Inumpy/core/src -Inumpy/core/include -I/home/ucapsag/enzo3/src/yt/doc/yt-x86_64/include/python2.6 -c' gcc: _configtest.c _configtest.c:1: warning: conflicting types for built-in function 'asin' _configtest.c:2: warning: conflicting types for built-in function 'cos' BUILDING MATPLOTLIB matplotlib: 0.99.1.1 python: 2.6.3 (r263:75183, Aug 19 2010, 20:38:01) [GCC 3.4.6 20060404 (Red Hat 3.4.6-11)] platform: linux2 REQUIRED DEPENDENCIES numpy: 1.3.0 freetype2: 9.7.3 OPTIONAL BACKEND DEPENDENCIES libpng: found, but unknown version (no pkg-config) * Could not find 'libpng' headers in any of * '/usr/local/include', '/usr/include', '.' Tkinter: Tkinter: 73770, Tk: 8.4, Tcl: 8.4 /usr/bin/ld: skipping incompatible /usr/lib/libm.so when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libm.a when searching for -lm /usr/bin/ld: skipping incompatible /usr/lib/libpthread.so when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libpthread.a when searching for -lpthread /usr/bin/ld: skipping incompatible /usr/lib/libc.so when searching for -lc /usr/bin/ld: skipping incompatible /usr/lib/libc.a when searching for -lc lib/matplotlib/delaunay/_delaunay.cpp: In function `PyObject* compute_planes_method(PyObject*, PyObject*)': lib/matplotlib/delaunay/_delaunay.cpp:315: warning: 'y' might be used uninitialized in this function cc1plus: warning: command line option "-Wstrict-prototypes" is valid for Ada/C/ObjC but not for C++ src/backend_agg.cpp:3:17: png.h: No such file or directory error: command 'gcc' failed with exit status 1 The last error seems to be the culprit?. -shankar
Hi Shankar,
Ah, yes! Bingo. Okay, fortunately it looks like at some point in the past I added libpng to the install script options. If you edit install_script.sh and turn on INST_PNG, when you re-run I think it will give a shot at installing libpng independently of the OS. I believe that'll fix the issue, but let me know how it goes? Thanks, Matt
Hi Matt, I may be having pre-yt1.7 scripts. So I tried the following 3 ways but they are all failing. 1. I svn'd a copy of enzo ... Checked out external at revision 1808. Checked out revision 3068. but the install_script.sh that comes with it does not have INST_PNG. 2. So I tried getting YT in my home directory independent of enzo like... [ucapsag@login03 ~]$ svn export http://svn.enzotools.org/yt/branches/yt-1.7/doc/install_script.sh svn: REPORT request failed on '/yt/!svn/vcc/default' svn: Cannot replace a directory from within 3. Finally, I got hold of http://bitbucket.org/MatthewTurk/yt/src/8190256cc360/doc/install_script.sh and put it in my enzo's yt (of step 1 above). It hangs saying... running install_egg_info Writing /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//lib/python2.6/lib-dynload/Python-2.6.3-py2.6.egg-info if test -f /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python -o -h /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python; \ then rm -f /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python; \ else true; \ fi (cd /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin; ln python2.6 python) rm -f /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin/python-config (cd /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//bin; ln -s python2.6-config python-config) Creating directory /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//share/man/man1 /usr/bin/install -c -m 644 ./Misc/python.man \ /home/ucapsag/enzo3/src/yt/doc/yt-x86_64//share/man/man1/python.1 /home/ucapsag/enzo3/src/yt/doc/yt-x86_64/bin/python2.6: can't open file '/home/ucapsag/enzo3/src/yt/distribute_setup.py': [Errno 2] No such file or directory shankar
Hi Shankar,
Youch! Okay, so here's my suggestion. The error with 1.7 seems to be that it won't replace an existing file. Just cd into your home directory, and do this: svn export http://svn.enzotools.org/yt/trunk/doc/install_script.sh Then, make sure there're no yt-i386 or yt-x86_64 directories or anything in your home directory. Then edit the script, set INST_PNG=1, and run: bash install_script.sh This should be totally clean. I'm going to try to disable the yt install script inside enzo, because we're moving away from that model of distribution. Anyway, let me know how that goes. Sorry this is so troublesome! -Matt
participants (2)
-
Agarwal, Shankar -
Matthew Turk