Hello, I successfully installed firedrake but when I try to test the firedrake installation i get this error: (firedrake) [msarrafj@caml-lin Software]$ python -c "import firedrake" Traceback (most recent call last): File "<string>", line 1, in <module> File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/firedrake/firedrake/__init__.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/firedrake/firedrake/__init__.py>", line 32, in <module> from pyop2 import op2 # noqa: F401 File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/__init__.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/__init__.py>", line 4, in <module> from pyop2.op2 import * # noqa File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/op2.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/op2.py>", line 42, in <module> from pyop2.base import i # noqa: F401 File "/home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/base.py <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/base.py>", line 57, in <module> from pyop2.sparsity import build_sparsity ImportError: /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so: <http://cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so:> undefined symbol: PetscMallocA Attached is the associated firedrake-install.log if it helps Thanks in advance for your help. Sincerely, Sarraf
Hi Mohammad, this is strange, everything looked to have installed fine.
ImportError: /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so: undefined symbol: PetscMallocA
What does: ldd /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so Say? Thanks, Lawrence
Dear Lawrence, I get: $ ldd /home/ cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007ffc197fc000) libpetsc.so.3.8 => /lib64/libpetsc.so.3.8 (0x00007f0bfb6b8000) libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007f0bfb18f000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0bfaf73000) libc.so.6 => /lib64/libc.so.6 (0x00007f0bfabb0000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f0bfa88d000) libsuperlu.so.5.1 => /lib64/libsuperlu.so.5.1 (0x00007f0bfa618000) libumfpack.so.5 => /lib64/libumfpack.so.5 (0x00007f0bfa363000) libklu.so.1 => /lib64/libklu.so.1 (0x00007f0bfa12e000) libcholmod.so.2 => /lib64/libcholmod.so.2 (0x00007f0bf9e42000) libamd.so.2 => /lib64/libamd.so.2 (0x00007f0bf9c38000) libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f0bf7767000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f0bf7429000) libm.so.6 => /lib64/libm.so.6 (0x00007f0bf7127000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0bf6f22000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0bf6c1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0bf6a04000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0bf6800000) /lib64/ld-linux-x86-64.so.2 (0x000055a8504ca000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f0bf65c4000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007f0bf59af000) libsuitesparseconfig.so.4 => /lib64/libsuitesparseconfig.so.4 (0x00007f0bf57ac000) libcolamd.so.2 => /lib64/libcolamd.so.2 (0x00007f0bf55a4000) libbtf.so.1 => /lib64/libbtf.so.1 (0x00007f0bf53a0000) libcamd.so.2 => /lib64/libcamd.so.2 (0x00007f0bf5194000) libccolamd.so.2 => /lib64/libccolamd.so.2 (0x00007f0bf4f88000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0bf4d60000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f0bf4b5b000) Thanks for your help, Mohammad Mohammad Sarraf Joshaghani Phone: +1-281-781-5331 On Fri, Apr 20, 2018 at 3:18 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
Hi Mohammad,
this is strange, everything looked to have installed fine.
ImportError: /home/cougarnet.uh.edu/msarrafj/Software/firedrake/
src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so: undefined symbol: PetscMallocA
What does:
ldd /home/cougarnet.uh.edu/msarrafj/Software/firedrake/ src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so
Say?
Thanks,
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 23 Apr 2018, at 20:57, Mohammad Sarraf Joshaghani <m.sarraf.j@gmail.com> wrote:
Dear Lawrence, I get:
$ ldd /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007ffc197fc000) libpetsc.so.3.8 => /lib64/libpetsc.so.3.8 (0x00007f0bfb6b8000)
This looks to be the problem, I think. Assuming that you got firedrake-install to install PETSc, it should be installed in: /home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib/.../petsc Whereas here it looks like the linker is picking up a system-installed PETSc. That dynamic library was linked as: gcc -pthread -shared -Wl,-z,relro -g build/temp.linux-x86_64-3.6/pyop2/sparsity.o -L/usr/lib64 -lpetsc -lpython3.6m -o /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so -L/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib -Wl,-rpath,/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib So we bake the rpath to PETSc in. But somehow when running, you don't pick that one up. Can you show the output of "env" in the same shell you ran "ldd" please? Cheers, Lawrence
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007f0bfb18f000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0bfaf73000) libc.so.6 => /lib64/libc.so.6 (0x00007f0bfabb0000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f0bfa88d000) libsuperlu.so.5.1 => /lib64/libsuperlu.so.5.1 (0x00007f0bfa618000) libumfpack.so.5 => /lib64/libumfpack.so.5 (0x00007f0bfa363000) libklu.so.1 => /lib64/libklu.so.1 (0x00007f0bfa12e000) libcholmod.so.2 => /lib64/libcholmod.so.2 (0x00007f0bf9e42000) libamd.so.2 => /lib64/libamd.so.2 (0x00007f0bf9c38000) libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f0bf7767000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f0bf7429000) libm.so.6 => /lib64/libm.so.6 (0x00007f0bf7127000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0bf6f22000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0bf6c1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0bf6a04000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0bf6800000) /lib64/ld-linux-x86-64.so.2 (0x000055a8504ca000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f0bf65c4000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007f0bf59af000) libsuitesparseconfig.so.4 => /lib64/libsuitesparseconfig.so.4 (0x00007f0bf57ac000) libcolamd.so.2 => /lib64/libcolamd.so.2 (0x00007f0bf55a4000) libbtf.so.1 => /lib64/libbtf.so.1 (0x00007f0bf53a0000) libcamd.so.2 => /lib64/libcamd.so.2 (0x00007f0bf5194000) libccolamd.so.2 => /lib64/libccolamd.so.2 (0x00007f0bf4f88000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0bf4d60000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f0bf4b5b000)
Hi Lawrence, These are the output of “env”: XDG_SESSION_ID=10842 HOSTNAME=caml-lin.cive.e.uh.edu TERM=xterm-256color SHELL=/bin/bash FIREDRAKE_TSFC_KERNEL_CACHE_DIR=/home/cougarnet.uh.edu/msarrafj/Software/cache-firedrake/tsfc HISTSIZE=1000 SSH_CLIENT=129.7.154.32 59265 22 OLDPWD=/home/cougarnet.uh.edu/msarrafj SSH_TTY=/dev/pts/1 QT_GRAPHICSSYSTEM_CHECKED=1 USER=msarrafj LD_LIBRARY_PATH=/usr/local/cuda/lib64 LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: VIRTUAL_ENV=/home/cougarnet.uh.edu/msarrafj/apps/firedrake MAIL=/var/spool/mail/msarrafj PATH=/home/cougarnet.uh.edu/msarrafj/apps/firedrake/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/cougarnet.uh.edu/msarrafj/.local/bin:/home/cougarnet.uh.edu/msarrafj/bin PYOP2_CACHE_DIR=/home/cougarnet.uh.edu/msarrafj/Software/cache-firedrake/pyop2 PWD=/home/cougarnet.uh.edu/msarrafj/apps LANG=en_US.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles LOADEDMODULES= PS1=(firedrake) [\u@\h \W]\$ HISTCONTROL=ignoredups KRB5CCNAME=FILE:/tmp/krb5cc_418246747_Pi8UI3 SHLVL=1 HOME=/home/cougarnet.uh.edu/msarrafj PETSC_CONFIGURE_OPTIONS=--download-ml LOGNAME=msarrafj XDG_DATA_DIRS=/home/cougarnet.uh.edu/msarrafj/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/ SSH_CONNECTION=129.7.154.32 59265 172.21.38.71 22 MODULESHOME=/usr/share/Modules LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/418246747 BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env Thanks, Mohammad
On Apr 24, 2018, at 2:55 AM, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> wrote:
On 23 Apr 2018, at 20:57, Mohammad Sarraf Joshaghani <m.sarraf.j@gmail.com> wrote:
Dear Lawrence, I get:
$ ldd /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007ffc197fc000) libpetsc.so.3.8 => /lib64/libpetsc.so.3.8 (0x00007f0bfb6b8000)
This looks to be the problem, I think. Assuming that you got firedrake-install to install PETSc, it should be installed in:
/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib/.../petsc
Whereas here it looks like the linker is picking up a system-installed PETSc.
That dynamic library was linked as:
gcc -pthread -shared -Wl,-z,relro -g build/temp.linux-x86_64-3.6/pyop2/sparsity.o -L/usr/lib64 -lpetsc -lpython3.6m -o /home/cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so -L/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib -Wl,-rpath,/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib
So we bake the rpath to PETSc in. But somehow when running, you don't pick that one up.
Can you show the output of "env" in the same shell you ran "ldd" please?
Cheers,
Lawrence
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007f0bfb18f000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0bfaf73000) libc.so.6 => /lib64/libc.so.6 (0x00007f0bfabb0000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f0bfa88d000) libsuperlu.so.5.1 => /lib64/libsuperlu.so.5.1 (0x00007f0bfa618000) libumfpack.so.5 => /lib64/libumfpack.so.5 (0x00007f0bfa363000) libklu.so.1 => /lib64/libklu.so.1 (0x00007f0bfa12e000) libcholmod.so.2 => /lib64/libcholmod.so.2 (0x00007f0bf9e42000) libamd.so.2 => /lib64/libamd.so.2 (0x00007f0bf9c38000) libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f0bf7767000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f0bf7429000) libm.so.6 => /lib64/libm.so.6 (0x00007f0bf7127000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0bf6f22000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0bf6c1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0bf6a04000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0bf6800000) /lib64/ld-linux-x86-64.so.2 (0x000055a8504ca000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f0bf65c4000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007f0bf59af000) libsuitesparseconfig.so.4 => /lib64/libsuitesparseconfig.so.4 (0x00007f0bf57ac000) libcolamd.so.2 => /lib64/libcolamd.so.2 (0x00007f0bf55a4000) libbtf.so.1 => /lib64/libbtf.so.1 (0x00007f0bf53a0000) libcamd.so.2 => /lib64/libcamd.so.2 (0x00007f0bf5194000) libccolamd.so.2 => /lib64/libccolamd.so.2 (0x00007f0bf4f88000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0bf4d60000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f0bf4b5b000)
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Mohammad, I think your system administrator mucked something up when he was attempting to install firedrake (or just PETSc) himself. He might have made an instance of PETSc some time ago. If I recall correctly he had the same error as you. Ask and see if he can “clean” everything. Like, remove any instances of PETSc he may have created. Or better yet, have him give you root access since it’s your machine. On Tue, Apr 24, 2018 at 2:27 PM, Mohammad Sarraf Joshaghani < m.sarraf.j@gmail.com> wrote:
Hi Lawrence, These are the output of “env”:
XDG_SESSION_ID=10842 HOSTNAME=caml-lin.cive.e.uh.edu TERM=xterm-256color SHELL=/bin/bash FIREDRAKE_TSFC_KERNEL_CACHE_DIR=/home/ cougarnet.uh.edu/msarrafj/Software/cache-firedrake/tsfc HISTSIZE=1000 SSH_CLIENT=129.7.154.32 59265 22 OLDPWD=/home/cougarnet.uh.edu/msarrafj SSH_TTY=/dev/pts/1 QT_GRAPHICSSYSTEM_CHECKED=1 USER=msarrafj LD_LIBRARY_PATH=/usr/local/cuda/lib64
LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40;38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5;232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48;5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48;5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5;34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*.taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38;5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*.zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*.lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5;9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb=38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9:*.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo=38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:*.jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*.pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*.xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*.png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*.pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*.m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*.mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*.qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*.rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*.fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf=38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf=38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx=38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38;5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5;45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*.oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: VIRTUAL_ENV=/home/cougarnet.uh.edu/msarrafj/apps/firedrake MAIL=/var/spool/mail/msarrafj PATH=/home/ cougarnet.uh.edu/msarrafj/apps/firedrake/bin:/usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/cougarnet.uh.edu/msarrafj/.local/bin:/home/cougarnet.uh.edu/msarrafj/bin PYOP2_CACHE_DIR=/home/ cougarnet.uh.edu/msarrafj/Software/cache-firedrake/pyop2 PWD=/home/cougarnet.uh.edu/msarrafj/apps LANG=en_US.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles LOADEDMODULES= PS1=(firedrake) [\u@\h \W]\$ HISTCONTROL=ignoredups KRB5CCNAME=FILE:/tmp/krb5cc_418246747_Pi8UI3 SHLVL=1 HOME=/home/cougarnet.uh.edu/msarrafj PETSC_CONFIGURE_OPTIONS=--download-ml LOGNAME=msarrafj XDG_DATA_DIRS=/home/ cougarnet.uh.edu/msarrafj/.local/share/flatpak/exports/share/:/var/lib/flatpak/exports/share/:/usr/local/share/:/usr/share/ SSH_CONNECTION=129.7.154.32 59265 172.21.38.71 22 MODULESHOME=/usr/share/Modules LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/418246747 BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env
Thanks, Mohammad
On Apr 24, 2018, at 2:55 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
On 23 Apr 2018, at 20:57, Mohammad Sarraf Joshaghani <m.sarraf.j@gmail.com> wrote:
Dear Lawrence, I get:
$ ldd /home/ cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007ffc197fc000) libpetsc.so.3.8 => /lib64/libpetsc.so.3.8 (0x00007f0bfb6b8000)
This looks to be the problem, I think. Assuming that you got firedrake-install to install PETSc, it should be installed in:
/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib/.../petsc
Whereas here it looks like the linker is picking up a system-installed PETSc.
That dynamic library was linked as:
gcc -pthread -shared -Wl,-z,relro -g build/temp.linux-x86_64-3.6/pyop2/sparsity.o -L/usr/lib64 -lpetsc -lpython3.6m -o /home/ cougarnet.uh.edu/msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so -L/home/ cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib -Wl,-rpath,/home/ cougarnet.uh.edu/msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib
So we bake the rpath to PETSc in. But somehow when running, you don't pick that one up.
Can you show the output of "env" in the same shell you ran "ldd" please?
Cheers,
Lawrence
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007f0bfb18f000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0bfaf73000) libc.so.6 => /lib64/libc.so.6 (0x00007f0bfabb0000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f0bfa88d000) libsuperlu.so.5.1 => /lib64/libsuperlu.so.5.1 (0x00007f0bfa618000) libumfpack.so.5 => /lib64/libumfpack.so.5 (0x00007f0bfa363000) libklu.so.1 => /lib64/libklu.so.1 (0x00007f0bfa12e000) libcholmod.so.2 => /lib64/libcholmod.so.2 (0x00007f0bf9e42000) libamd.so.2 => /lib64/libamd.so.2 (0x00007f0bf9c38000) libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f0bf7767000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f0bf7429000) libm.so.6 => /lib64/libm.so.6 (0x00007f0bf7127000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0bf6f22000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0bf6c1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0bf6a04000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0bf6800000) /lib64/ld-linux-x86-64.so.2 (0x000055a8504ca000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f0bf65c4000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007f0bf59af000) libsuitesparseconfig.so.4 => /lib64/libsuitesparseconfig.so.4 (0x00007f0bf57ac000) libcolamd.so.2 => /lib64/libcolamd.so.2 (0x00007f0bf55a4000) libbtf.so.1 => /lib64/libbtf.so.1 (0x00007f0bf53a0000) libcamd.so.2 => /lib64/libcamd.so.2 (0x00007f0bf5194000) libccolamd.so.2 => /lib64/libccolamd.so.2 (0x00007f0bf4f88000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0bf4d60000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f0bf4b5b000)
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Thanks Justin. I asked system admin to remove all PETSc instances and will update you upon fresh install of firedrake. Mohammad Sarraf Joshaghani Phone: +1-281-781-5331 On Wed, Apr 25, 2018 at 9:12 AM, Justin Chang <jychang48@gmail.com> wrote:
Mohammad, I think your system administrator mucked something up when he was attempting to install firedrake (or just PETSc) himself. He might have made an instance of PETSc some time ago. If I recall correctly he had the same error as you.
Ask and see if he can “clean” everything. Like, remove any instances of PETSc he may have created. Or better yet, have him give you root access since it’s your machine.
On Tue, Apr 24, 2018 at 2:27 PM, Mohammad Sarraf Joshaghani < m.sarraf.j@gmail.com> wrote:
Hi Lawrence, These are the output of “env”:
XDG_SESSION_ID=10842 HOSTNAME=caml-lin.cive.e.uh.edu TERM=xterm-256color SHELL=/bin/bash FIREDRAKE_TSFC_KERNEL_CACHE_DIR=/home/cougarnet.uh.edu/ msarrafj/Software/cache-firedrake/tsfc HISTSIZE=1000 SSH_CLIENT=129.7.154.32 59265 22 OLDPWD=/home/cougarnet.uh.edu/msarrafj SSH_TTY=/dev/pts/1 QT_GRAPHICSSYSTEM_CHECKED=1 USER=msarrafj LD_LIBRARY_PATH=/usr/local/cuda/lib64 LS_COLORS=rs=0:di=38;5;27:ln=38;5;51:mh=44;38;5;15:pi=40; 38;5;11:so=38;5;13:do=38;5;5:bd=48;5;232;38;5;11:cd=48;5; 232;38;5;3:or=48;5;232;38;5;9:mi=05;48;5;232;38;5;15:su=48; 5;196;38;5;15:sg=48;5;11;38;5;16:ca=48;5;196;38;5;226:tw=48; 5;10;38;5;16:ow=48;5;10;38;5;21:st=48;5;21;38;5;15:ex=38;5; 34:*.tar=38;5;9:*.tgz=38;5;9:*.arc=38;5;9:*.arj=38;5;9:*. taz=38;5;9:*.lha=38;5;9:*.lz4=38;5;9:*.lzh=38;5;9:*.lzma=38; 5;9:*.tlz=38;5;9:*.txz=38;5;9:*.tzo=38;5;9:*.t7z=38;5;9:*. zip=38;5;9:*.z=38;5;9:*.Z=38;5;9:*.dz=38;5;9:*.gz=38;5;9:*. lrz=38;5;9:*.lz=38;5;9:*.lzo=38;5;9:*.xz=38;5;9:*.bz2=38;5; 9:*.bz=38;5;9:*.tbz=38;5;9:*.tbz2=38;5;9:*.tz=38;5;9:*.deb= 38;5;9:*.rpm=38;5;9:*.jar=38;5;9:*.war=38;5;9:*.ear=38;5;9: *.sar=38;5;9:*.rar=38;5;9:*.alz=38;5;9:*.ace=38;5;9:*.zoo= 38;5;9:*.cpio=38;5;9:*.7z=38;5;9:*.rz=38;5;9:*.cab=38;5;9:* .jpg=38;5;13:*.jpeg=38;5;13:*.gif=38;5;13:*.bmp=38;5;13:*. pbm=38;5;13:*.pgm=38;5;13:*.ppm=38;5;13:*.tga=38;5;13:*. xbm=38;5;13:*.xpm=38;5;13:*.tif=38;5;13:*.tiff=38;5;13:*. png=38;5;13:*.svg=38;5;13:*.svgz=38;5;13:*.mng=38;5;13:*. pcx=38;5;13:*.mov=38;5;13:*.mpg=38;5;13:*.mpeg=38;5;13:*. m2v=38;5;13:*.mkv=38;5;13:*.webm=38;5;13:*.ogm=38;5;13:*. mp4=38;5;13:*.m4v=38;5;13:*.mp4v=38;5;13:*.vob=38;5;13:*. qt=38;5;13:*.nuv=38;5;13:*.wmv=38;5;13:*.asf=38;5;13:*. rm=38;5;13:*.rmvb=38;5;13:*.flc=38;5;13:*.avi=38;5;13:*. fli=38;5;13:*.flv=38;5;13:*.gl=38;5;13:*.dl=38;5;13:*.xcf= 38;5;13:*.xwd=38;5;13:*.yuv=38;5;13:*.cgm=38;5;13:*.emf= 38;5;13:*.axv=38;5;13:*.anx=38;5;13:*.ogv=38;5;13:*.ogx= 38;5;13:*.aac=38;5;45:*.au=38;5;45:*.flac=38;5;45:*.mid=38; 5;45:*.midi=38;5;45:*.mka=38;5;45:*.mp3=38;5;45:*.mpc=38;5; 45:*.ogg=38;5;45:*.ra=38;5;45:*.wav=38;5;45:*.axa=38;5;45:*. oga=38;5;45:*.spx=38;5;45:*.xspf=38;5;45: VIRTUAL_ENV=/home/cougarnet.uh.edu/msarrafj/apps/firedrake MAIL=/var/spool/mail/msarrafj PATH=/home/cougarnet.uh.edu/msarrafj/apps/firedrake/bin:/ usr/lib64/openmpi/bin:/usr/local/cuda/bin:/usr/local/bin: /usr/bin:/usr/local/sbin:/usr/sbin:/home/cougarnet.uh.edu/ msarrafj/.local/bin:/home/cougarnet.uh.edu/msarrafj/bin PYOP2_CACHE_DIR=/home/cougarnet.uh.edu/msarrafj/Software/ cache-firedrake/pyop2 PWD=/home/cougarnet.uh.edu/msarrafj/apps LANG=en_US.UTF-8 MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles LOADEDMODULES= PS1=(firedrake) [\u@\h \W]\$ HISTCONTROL=ignoredups KRB5CCNAME=FILE:/tmp/krb5cc_418246747_Pi8UI3 SHLVL=1 HOME=/home/cougarnet.uh.edu/msarrafj PETSC_CONFIGURE_OPTIONS=--download-ml LOGNAME=msarrafj XDG_DATA_DIRS=/home/cougarnet.uh.edu/msarrafj/.local/share/ flatpak/exports/share/:/var/lib/flatpak/exports/share/:/ usr/local/share/:/usr/share/ SSH_CONNECTION=129.7.154.32 59265 172.21.38.71 22 MODULESHOME=/usr/share/Modules LESSOPEN=||/usr/bin/lesspipe.sh %s XDG_RUNTIME_DIR=/run/user/418246747 BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*` } _=/usr/bin/env
Thanks, Mohammad
On Apr 24, 2018, at 2:55 AM, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
On 23 Apr 2018, at 20:57, Mohammad Sarraf Joshaghani < m.sarraf.j@gmail.com> wrote:
Dear Lawrence, I get:
$ ldd /home/cougarnet.uh.edu/msarrafj/Software/firedrake/ src/PyOP2/pyop2/sparsity.cpython-36m-x86_64-linux-gnu.so linux-vdso.so.1 => (0x00007ffc197fc000) libpetsc.so.3.8 => /lib64/libpetsc.so.3.8 (0x00007f0bfb6b8000)
This looks to be the problem, I think. Assuming that you got firedrake-install to install PETSc, it should be installed in:
/home/cougarnet.uh.edu/msarrafj/Software/firedrake/lib/.../petsc
Whereas here it looks like the linker is picking up a system-installed PETSc.
That dynamic library was linked as:
gcc -pthread -shared -Wl,-z,relro -g build/temp.linux-x86_64-3.6/pyop2/sparsity.o -L/usr/lib64 -lpetsc -lpython3.6m -o /home/cougarnet.uh.edu/ msarrafj/Software/firedrake/src/PyOP2/pyop2/sparsity. cpython-36m-x86_64-linux-gnu.so -L/home/cougarnet.uh.edu/ msarrafj/Software/firedrake/lib64/python3.6/site-packages/petsc/lib -Wl,-rpath,/home/cougarnet.uh.edu/msarrafj/Software/ firedrake/lib64/python3.6/site-packages/petsc/lib
So we bake the rpath to PETSc in. But somehow when running, you don't pick that one up.
Can you show the output of "env" in the same shell you ran "ldd" please?
Cheers,
Lawrence
libpython3.6m.so.1.0 => /lib64/libpython3.6m.so.1.0 (0x00007f0bfb18f000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f0bfaf73000) libc.so.6 => /lib64/libc.so.6 (0x00007f0bfabb0000) libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f0bfa88d000) libsuperlu.so.5.1 => /lib64/libsuperlu.so.5.1 (0x00007f0bfa618000) libumfpack.so.5 => /lib64/libumfpack.so.5 (0x00007f0bfa363000) libklu.so.1 => /lib64/libklu.so.1 (0x00007f0bfa12e000) libcholmod.so.2 => /lib64/libcholmod.so.2 (0x00007f0bf9e42000) libamd.so.2 => /lib64/libamd.so.2 (0x00007f0bf9c38000) libopenblas.so.0 => /lib64/libopenblas.so.0 (0x00007f0bf7767000) libX11.so.6 => /lib64/libX11.so.6 (0x00007f0bf7429000) libm.so.6 => /lib64/libm.so.6 (0x00007f0bf7127000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f0bf6f22000) libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f0bf6c1a000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f0bf6a04000) libutil.so.1 => /lib64/libutil.so.1 (0x00007f0bf6800000) /lib64/ld-linux-x86-64.so.2 (0x000055a8504ca000) libquadmath.so.0 => /lib64/libquadmath.so.0 (0x00007f0bf65c4000) libsatlas.so.3 => /usr/lib64/atlas/libsatlas.so.3 (0x00007f0bf59af000) libsuitesparseconfig.so.4 => /lib64/libsuitesparseconfig.so.4 (0x00007f0bf57ac000) libcolamd.so.2 => /lib64/libcolamd.so.2 (0x00007f0bf55a4000) libbtf.so.1 => /lib64/libbtf.so.1 (0x00007f0bf53a0000) libcamd.so.2 => /lib64/libcamd.so.2 (0x00007f0bf5194000) libccolamd.so.2 => /lib64/libccolamd.so.2 (0x00007f0bf4f88000) libxcb.so.1 => /lib64/libxcb.so.1 (0x00007f0bf4d60000) libXau.so.6 => /lib64/libXau.so.6 (0x00007f0bf4b5b000)
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participants (3)
-
Justin Chang
-
Lawrence Mitchell
-
Mohammad Sarraf Joshaghani