[CIG-SHORT] Help with installing Pylith

Mon Oct 4 14:53:35 PDT 2010

Hi Birendra,

I'm at a conference so I haven't really been following this.  I guess one thing to check is whether the symbol is actually there.  If you go to the directory where open-mpi is installed, and then go to the lib directory, try the following:

nm libmpi.so | grep ompi_mpi_group_null

When I do this on my Linux machine, I get:

00000000002a39e0 B ompi_mpi_group_null

What do you get?

Charles

On 5/10/2010, at 3:19 AM, Birendra jha wrote:

> 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
> 
> 
> 
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Charles A. Williams
Scientist
GNS Science
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PO Box 30368
Lower Hutt  5040
New Zealand
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fax (office): 0064-4570-4600
C.Williams at gns.cri.nz
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