[CIG-SHORT] Help with installing Pylith

Mon Oct 4 07:19:08 PDT 2010

Hi Brad,

Thanks for your quick reply. I still couldn't fix it. I removed old nemesis-dev folder, created a new one, ran configure again, then make again and got errors during make. 

bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$ $HOME/src/nemesis-dev/configure --prefix=${TOOLS_DIR} CC=mpicc
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of mpicc... gcc3
checking for a Python interpreter with version >= 2.3... python
checking for python... /usr/bin/python
checking for python version... 2.6
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.6/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.6/site-packages
checking python config... ok
checking for python include directory... /usr/include/python2.6
checking how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking Python.h usability... yes
checking Python.h presence... yes
checking for Python.h... yes
checking whether -lpython2.6 is a shared library... yes
configure: downloading missing Python dependencies
configure: building Python dependencies
checking for egg-related flags... ok
checking for library containing MPI_Init... none required
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
configure: creating ./config.status
config.status: creating Makefile
config.status: creating config.h
config.status: executing depfiles commands
bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$ make
make  all-am
make[1]: Entering directory `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
mpicc -DHAVE_CONFIG_H -I. -I/home/bjha/src/nemesis-dev  -I/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg -I/usr/include/python2.6 -I/usr/include/python2.6   -g -O2 -MT nemesis.o -MD -MP -MF .deps/nemesis.Tpo -c -o nemesis.o /home/bjha/src/nemesis-dev/nemesis.c
mv -f .deps/nemesis.Tpo .deps/nemesis.Po
mpicc  -g -O2 -L/usr/lib -L/usr/lib/python2.6/config  -o nemesis nemesis.o  -lpthread -ldl -lutil -lm -lpython2.6
nemesis.o: In function `__pyx_f_4_mpi_9MPI_Group___init__':
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:175: undefined reference to `ompi_mpi_group_null'
nemesis.o: In function `__pyx_f_4_mpi_8MPI_Comm___init__':
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:102: undefined reference to `ompi_mpi_comm_null'
nemesis.o: In function `__pyx_f_4_mpi_getGroupObj':
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:384: undefined reference to `ompi_mpi_group_null'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:394: undefined reference to `ompi_mpi_group_empty'
nemesis.o: In function `init_mpi':
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1535: undefined reference to `ompi_mpi_comm_world'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1540: undefined reference to `ompi_mpi_comm_null'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1545: undefined reference to `ompi_mpi_comm_self'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1550: undefined reference to `ompi_mpi_group_null'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1555: undefined reference to `ompi_mpi_group_empty'
nemesis.o: In function `__pyx_f_4_mpi_getCommObj':
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:318: undefined reference to `ompi_mpi_comm_world'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:328: undefined reference to `ompi_mpi_comm_null'
/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:338: undefined reference to `ompi_mpi_comm_self'
collect2: ld returned 1 exit status
make[1]: *** [nemesis] Error 1
make[1]: Leaving directory `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
make: *** [all] Error 2
bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$ 

Please advise.

Thanks & best regards
Birendra

--- On Mon, 10/4/10, Brad Aagaard <baagaard at usgs.gov> wrote:

From: Brad Aagaard <baagaard at usgs.gov>
Subject: Re: [CIG-SHORT] Help with installing Pylith
To: cig-short at geodynamics.org
Date: Monday, October 4, 2010, 5:59 AM

Birendra-

Use mpicc as the C compiler to build nemesis (set CC=mpicc as a command 
line argument to configure). Using mpicc from OpenMPI will automatically 
add the command line options appropriate for compiling and linking with 
the MPI libraries.

Brad

On 10/3/10 4:57 PM, Birendra jha wrote:
> Dear developers,
> I am following the instructions on "Linux_ubuntu-AMD64_Aagaard.txt" to
> install pylith on Ubuntu 10.04 (through VMWare on my Windows XP 32bit).
> I am stuck at Step 8 during nemesis make:
> bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$
> <mailto:bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$> make
> make all-am
> make[1]: Entering directory
> `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
> gcc -DHAVE_CONFIG_H -I. -I/home/bjha/src/nemesis-dev
> -I/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg
> -I/usr/include/python2.6 -I/usr/include/python2.6
> -I/home/bjha/tools/gcc-4.4.1_64/include -g -O2 -MT nemesis.o -MD -MP -MF
> .deps/nemesis.Tpo -c -o nemesis.o /home/bjha/src/nemesis-dev/nemesis.c
> mv -f .deps/nemesis.Tpo .deps/nemesis.Po
> gcc -g -O2 -L/usr/lib -L/usr/lib/python2.6/config -o nemesis nemesis.o
> -lpthread -ldl -lutil -lm -lpython2.6
> nemesis.o: In function `__pyx_f_4_mpi_9MPI_Group___init__':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:175:
> undefined reference to `ompi_mpi_group_null'
> nemesis.o: In function `__pyx_f_4_mpi_8MPI_Comm___init__':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:102:
> undefined reference to `ompi_mpi_comm_null'
> nemesis.o: In function `__pyx_f_4_mpi_getGroupObj':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:384:
> undefined reference to `ompi_mpi_group_null'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:394:
> undefined reference to `ompi_mpi_group_empty'
> nemesis.o: In function `init_mpi':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1535:
> undefined reference to `ompi_mpi_comm_world'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1540:
> undefined reference to `ompi_mpi_comm_null'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1545:
> undefined reference to `ompi_mpi_comm_self'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1550:
> undefined reference to `ompi_mpi_group_null'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1555:
> undefined reference to `ompi_mpi_group_empty'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Error_string':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:793:
> undefined reference to `MPI_Error_string'
> nemesis.o: In function `__pyx_f_4_mpi_8MPI_Comm___dealloc__':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:132:
> undefined reference to `MPI_Comm_free'
> nemesis.o: In function `__pyx_f_4_mpi_9MPI_Group___dealloc__':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:205:
> undefined reference to `MPI_Group_free'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Barrier':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:493:
> undefined reference to `MPI_Barrier'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Comm_create':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:551:
> undefined reference to `MPI_Comm_create'
> nemesis.o: In function `__pyx_f_4_mpi_getCommObj':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:318:
> undefined reference to `ompi_mpi_comm_world'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:328:
> undefined reference to `ompi_mpi_comm_null'
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:338:
> undefined reference to `ompi_mpi_comm_self'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Comm_group':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:610:
> undefined reference to `MPI_Comm_group'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Comm_rank':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:673:
> undefined reference to `MPI_Comm_rank'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Comm_size':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:730:
> undefined reference to `MPI_Comm_size'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Group_excl':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:914:
> undefined reference to `MPI_Group_excl'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Group_incl':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1014:
> undefined reference to `MPI_Group_incl'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Group_rank':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1076:
> undefined reference to `MPI_Group_rank'
> nemesis.o: In function `__pyx_f_4_mpi_MPI_Group_size':
> /home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev/python/pythia-0.8.1.11-py2.6.egg/mpi/_mpi.c:1133:
> undefined reference to `MPI_Group_size'
> collect2: ld returned 1 exit status
> make[1]: *** [nemesis] Error 1
> make[1]: Leaving directory
> `/home/bjha/scratch/build/gcc-4.4.1_64/nemesis-dev'
> make: *** [all] Error 2
> bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$
> <mailto:bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/nemesis-dev$>
> Nemesis depends on MPI, but I noticed that in this set of instructions
> we don't install mpich2, but install OpenMPI (in contrast to
> "Linux_Fedora8-AMD64_Aagaard.txt" and "MacBookPro_Aagaard.txt"). Does
> that have to do something with my getting stuck during nemesis make? It
> is looking for ompi stuff, does that mean I am not linking it properly?
> Should I specify
> CPPFLAGS="-I${CIG_INCDIR} -I${MPI_INCDIR}" LDFLAGS="-L${CIG_LIBDIR}
> -L${MPI_LIBDIR}" LIBS="-lpmpich -lmpich"
> or
> CPPFLAGS="-I${CIG_INCDIR} -I${MPI_INCDIR}" LDFLAGS="-L${CIG_LIBDIR}
> -L${MPI_LIBDIR}" LIBS="-lpthread -lrt"
> during nemesis configure on Ubuntu (as it is for Macbook or Fedora,
> respectively)?
> During nemesis configure, I changed
> $HOME/src/nemesis-dev/configure --prefix=${TOOLS_DIR}
> to
> $HOME/src/nemesis-dev/configure --prefix=${TOOLS_DIR}
> CPPFLAGS="-I${TOOLS_DIR}/include"
> to be able to locate mpi.h because otherwise I getting "mpi.h not found"
> error during configure.
> Step 3.
> I got some errors during make install:
> bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/spatialdata$make
> <mailto:bjha at ubuntu:~/scratch/build/gcc-4.4.1_64/spatialdata$make> install
> ...(lots of stuff scrolled by)...
> Processing dependencies for spatialdata==0.6.0
> Traceback (most recent call last):
> File "setup.py", line 36, in <module>
> url = 'http://www.geodynamics.org/',
> File "/usr/lib/python2.6/distutils/core.py", line 152, in setup
> dist.run_commands()
> File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands
> self.run_command(cmd)
> File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
> cmd_obj.run()
> File
> "/home/bjha/src/spatialdata/merlin-1.7.egg/merlin/command/install_deps.py",
> line 25, in run
> File
> "/home/bjha/src/spatialdata/merlin-1.7.egg/merlin/command/install_deps.py",
> line 74, in install_dependencies
> File
> "/home/bjha/src/spatialdata/merlin-1.7.egg/merlin/command/easy_install.py",
> line 526, in process_distribution
> File "/home/bjha/src/spatialdata/merlin-1.7.egg/merlin/__init__.py",
> line 650, in resolve
>
> File "/home/bjha/src/spatialdata/merlin-1.7.egg/merlin/__init__.py",
> line 2219, in requires
>
> merlin.UnknownExtra: pythia 0.8.1.10 has no such extra feature 'mpi'
> make[3]: *** [install-data-hook] Error 1
> make[3]: Leaving directory
> `/home/bjha/scratch/build/gcc-4.4.1_64/spatialdata'
> make[2]: *** [install-data-am] Error 2
> make[2]: Leaving directory
> `/home/bjha/scratch/build/gcc-4.4.1_64/spatialdata'
> make[1]: *** [install-am] Error 2
> make[1]: Leaving directory
> `/home/bjha/scratch/build/gcc-4.4.1_64/spatialdata'
> make: *** [install-recursive] Error 1
> But I went ahead with mpicc -show which gives:
> gcc -I/home/bjha/tools/gcc-4.4.1_64/include -pthread
> -L/home/bjha/tools/gcc-4.4.1_64/lib -lmpi -lopen-rte -lopen-pal -ldl
> -Wl,--export-dynamic -lnsl -lutil -lm -ldl
> Does that look ok to you?
> Step 6.
> I replaced spatialdata-dev with spatialdata, because I didn't find
> spatiaaldata-dev in the repository.
> I really need your help!
> Thank you & best regards
> Birendra