I am trying to install fenics on an Ubuntu 12.04 cluster,
without root permissions.
My home-directory is on afs, and not big enough to install
in. I am instead trying to install in a non-backed up parallel filesystem
called pfs. I am having some problems setting the directory. I tried
downloading fenics-install.sh and making some changes:
#export PROFILE_INSTALL_DIR=\$HOME/.hashdist/bld/profile/\$PROFILE
export
PROFILE_INSTALL_DIR=/pfs/nobackup/home/b/bbrydsoe/fenics_install/.hashdist/bld/profile/\$PROFILE
but that did not seem to help. Regardless I got the same error as I did
when running fenics-install.sh without downloading first. Tail of
build.log:
2015/02/04 15:24:21 - INFO: [package:run_job] make[1]: Leaving directory
`/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/ncurses-viognkgus4nj/form'
2015/02/04 15:24:21 - INFO: [package:run_job] cd misc && make DESTDIR=""
install
2015/02/04 15:24:21 - INFO: [package:run_job] make[1]: Entering directory
`/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/ncurses-viognkgus4nj/misc'
2015/02/04 15:24:21 - INFO: [package:run_job] mkdir -p
/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share
2015/02/04 15:24:21 - INFO: [package:run_job] mkdir -p
/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/tabset
2015/02/04 15:24:21 - INFO: [package:run_job] DESTDIR= \
2015/02/04 15:24:21 - INFO: [package:run_job]
prefix=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj
\
2015/02/04 15:24:21 - INFO: [package:run_job]
exec_prefix=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj
\
2015/02/04 15:24:21 - INFO: [package:run_job]
bindir=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/bin
\
2015/02/04 15:24:21 - INFO: [package:run_job] top_srcdir=.. \
2015/02/04 15:24:21 - INFO: [package:run_job] srcdir=. \
2015/02/04 15:24:21 - INFO: [package:run_job]
datadir=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share
\
2015/02/04 15:24:21 - INFO: [package:run_job]
ticdir=/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/terminfo
\
2015/02/04 15:24:21 - INFO: [package:run_job] source=terminfo.tmp \
2015/02/04 15:24:21 - INFO: [package:run_job] cross_compiling=no \
2015/02/04 15:24:21 - INFO: [package:run_job] /bin/sh ./run_tic.sh
2015/02/04 15:24:21 - INFO: [package:run_job] ** Building terminfo
database, please wait...
2015/02/04 15:24:21 - INFO: [package:run_job] Running sh ./shlib tic to
install
/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/terminfo
...
2015/02/04 15:24:21 - INFO: [package:run_job]
2015/02/04 15:24:21 - INFO: [package:run_job] You may see messages
regarding extended capabilities, e.g., AX.
2015/02/04 15:24:21 - INFO: [package:run_job] These are extended
terminal capabilities which are compiled
2015/02/04 15:24:21 - INFO: [package:run_job] using
2015/02/04 15:24:21 - INFO: [package:run_job] tic -x
2015/02/04 15:24:21 - INFO: [package:run_job] If you have ncurses 4.2
applications, you should read the INSTALL
2015/02/04 15:24:21 - INFO: [package:run_job] document, and install the
terminfo without the -x option.
2015/02/04 15:24:21 - INFO: [package:run_job]
2015/02/04 15:24:22 - INFO: [package:run_job] "terminfo.tmp", line 306,
terminal 'lpr': can't link l/lpr to p/printer
2015/02/04 15:24:22 - INFO: [package:run_job] ? tic could not build
/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/bld/ncurses/viognkgus4nj/share/terminfo
2015/02/04 15:24:22 - INFO: [package:run_job] make[1]: *** [install.data]
Error 1
2015/02/04 15:24:22 - INFO: [package:run_job] make[1]: Leaving directory
`/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/ncurses-viognkgus4nj/misc'
2015/02/04 15:24:22 - INFO: [package:run_job] make: *** [install] Error 2
2015/02/04 15:24:22 - ERROR: [package:run_job] Command '[u'/bin/bash',
'_hashdist/build.sh']' returned non-zero exit status 2
2015/02/04 15:24:22 - ERROR: [package:run_job] command failed (code=2);
raising
I then downloaded hashdist and hashstack too, and created my own profile:
extends:
- name: hashstack
urls: ['https://github.com/hashdist/hashstack.git']
key: 'git:1a97d560b12d86d8c36f8e574a1ebb3ea00067b7'
file: debian.yaml
parameters:
HOST_MPICC: /lap/openmpi/1.6.5/gcc-4.6/bin/mpicc
HOST_MPICXX: /lap/openmpi/1.6.5/gcc-4.6/bin/mpic++
HOST_MPIF77: /lap/openmpi/1.6.5/gcc-4.6/bin/mpif77
HOST_MPIF90: /lap/openmpi/1.6.5/gcc-4.6/bin/mpif90
HOST_MPIEXEC: /lap/openmpi/1.6.5/gcc-4.6/bin/mpiexec
HOST_CMAKE: /lap/cmake/2.8.12.1/bin/cmake
HOST_PYTHON: /usr/bin/python
HOST_SWIG_EXECUTABLE: /usr/bin/swig
HOST_PETSC_DIR: /lap/petsc/3.4.3/gcc/ompi/opt
HOST_PETSC_ARCH: linux-gnu-c-opt
HOST_SLEPC_DIR: /lap/slepc/3.4.3/gcc/ompi/opt
HOST_BLAS_DIR: /lap/openblas/0.2.9/lib/gcc
packages:
blas:
use: host-blas
# alternative to system blas:
# use: openblas
mpi:
# On debian: apt-get install mpich
use: host-mpi
# alternative to system mpi:
# use: openmpi
zlib:
nose:
launcher:
jinja2:
python:
host: true
use_python_host_packages: true
numpy:
use: host-numpy
cmake:
use: host-cmake
petsc:
use: host-petsc
slepc:
swig:
use: host-swig
boost:
toolset: gcc
address_model: 64
dolfin:
build_with: |
suitesparse, scotch, parmetis, petsc, slepc, zlib, hdf5, vtk
and did
hit build
I know get errors while building vtk. Last part of the build.log:
2015/02/05 12:57:12 - INFO: [package:run_job] CMake Warning (dev) in
Geovis/CMakeLists.txt:
2015/02/05 12:57:12 - INFO: [package:run_job] Policy CMP0022 is not set:
INTERFACE_LINK_LIBRARIES defines the link
2015/02/05 12:57:12 - INFO: [package:run_job] interface. Run "cmake
--help-policy CMP0022" for policy details. Use the
2015/02/05 12:57:12 - INFO: [package:run_job] cmake_policy command to
set the policy and suppress this warning.
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] Target "vtkGeovis" has an
INTERFACE_LINK_LIBRARIES property which differs
2015/02/05 12:57:12 - INFO: [package:run_job] from its
LINK_INTERFACE_LIBRARIES properties.
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] INTERFACE_LINK_LIBRARIES:
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job]
vtkWidgets;vtkViews;vtkproj4;vtkWidgets;vtkViews
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] LINK_INTERFACE_LIBRARIES:
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] vtkWidgets;vtkViews
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] This warning is for project
developers. Use -Wno-dev to suppress it.
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] CMake Warning (dev) in
Charts/CMakeLists.txt:
2015/02/05 12:57:12 - INFO: [package:run_job] Policy CMP0022 is not set:
INTERFACE_LINK_LIBRARIES defines the link
2015/02/05 12:57:12 - INFO: [package:run_job] interface. Run "cmake
--help-policy CMP0022" for policy details. Use the
2015/02/05 12:57:12 - INFO: [package:run_job] cmake_policy command to
set the policy and suppress this warning.
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] Target "vtkCharts" has an
INTERFACE_LINK_LIBRARIES property which differs
2015/02/05 12:57:12 - INFO: [package:run_job] from its
LINK_INTERFACE_LIBRARIES properties.
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] INTERFACE_LINK_LIBRARIES:
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job]
vtkViews;vtkftgl;vtkViews
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] LINK_INTERFACE_LIBRARIES:
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] vtkViews
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] This warning is for project
developers. Use -Wno-dev to suppress it.
2015/02/05 12:57:12 - INFO: [package:run_job]
2015/02/05 12:57:12 - INFO: [package:run_job] -- Configuring incomplete,
errors occurred!
2015/02/05 12:57:12 - INFO: [package:run_job] See also
"/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/vtk-izqbwqpiwzwf/_build/CMakeFiles/CMakeOutput.log".
2015/02/05 12:57:12 - INFO: [package:run_job] See also
"/afs/hpc2n.umu.se/home/b/bbrydsoe/.hashdist/tmp/vtk-izqbwqpiwzwf/_build/CMakeFiles/CMakeError.log".
2015/02/05 12:57:12 - ERROR: [package:run_job] Command '[u'/bin/bash',
'_hashdist/build.sh']' returned non-zero exit status 1
2015/02/05 12:57:12 - ERROR: [package:run_job] command failed (code=1);
raising
I have no idea what is going on. Any ideas?
-Birgitte
--
Birgitte Maria E. Brydsö
HPC2N, MIT-Huset
Umeå University
SE-901 87 Umeå
Telephone: +46(0)90-786 64 55
Email: [email protected]
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