Re^2: OpenMPI and Perl

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Re^3: OpenMPI and Perl by spadacciniweb (Curate) on Nov 24, 2009 at 15:50 UTC
Few later, update this question... As almut has written, I have recompiled OpenMPI lib, and it fix the problem. Thank you, Mariano (($_="Mzz ojjdloobnf jt uvy5502383")=~y~b-zg2-5c96-81~a-z0-9~s)=~s~~~s; print	[reply]
Re^4: OpenMPI and Perl by Vlad, the IM-perler (Novice) on Apr 16, 2010 at 06:40 UTC
I am having the same problem as tux300181 (it seems to be reported a bit recently) However none of the published fixes appear to be working. The symptom is: `[vlad@bd01 Parallel-MPI-Simple-0.03]$ make test PERL_DL_NONLAZY=1 /usr/bin/perl "-Iblib/lib" "-Iblib/arch" test.pl Can't load 'blib/arch/auto/Parallel/MPI/Simple/Simple.so' for module P +arallel::MPI::Simple: blib/arch/auto/Parallel/MPI/Simple/Simple.so: u +ndefined symbol: ompi_mpi_char at /usr/lib64/perl5/5.10.0/x86_64-linu +x-thread-multi/DynaLoader.pm line 203. at ic.pl line 3` [download] This appears to be a loader problem, although I am not sure, any assistance is greatly appreciated. What I did: perl Makefile.PL CC=mpicc CCFLAGS="-lopenmpi -m64 -L/usr/local/lib/ope +nmpi -L/usr/local/lib/" LIB=/usr/local/lib [vlad@bd01 Parallel-MPI-Simple-0.03]$ make mpicc -c -lopenmpi -m64 -L/usr/local/lib/openmpi -L/usr/local/lib/ - +O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protec +tor --param=ssp-buffer-size=4 -m64 -mtune=generic -DVERSION=\"0.03\ +" -DXS_VERSION=\"0.03\" -fPIC "-I/usr/lib64/perl5/5.10.0/x86_64-linux +-thread-multi/CORE" Simple.c Simple.xs: In function ‘_Gather’: Simple.xs:131: warning: null argument where non-null required (argumen +t 3) Simple.xs:124: warning: unused variable ‘rank’ Simple.xs: In function ‘_Comm_split’: Simple.xs:204: warning: unused variable ‘realcolour’ Simple.c: In function ‘Finalize’: Simple.xs:111: warning: control reaches end of non-void function Simple.c: In function ‘Barrier’: Simple.xs:106: warning: control reaches end of non-void function Simple.c: In function ‘Init’: Simple.xs:82: warning: control reaches end of non-void function Simple.c: In function ‘_Gather’: Simple.xs:160: warning: ‘buf_lens’ may be used uninitialized in this f +unction Running Mkbootstrap for Parallel::MPI::Simple () chmod 644 Simple.bs rm -f blib/arch/auto/Parallel/MPI/Simple/Simple.so gcc -shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions - +fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic Simple +.o -o blib/arch/auto/Parallel/MPI/Simple/Simple.so \ \ chmod 755 blib/arch/auto/Parallel/MPI/Simple/Simple.so cp Simple.bs blib/arch/auto/Parallel/MPI/Simple/Simple.bs chmod 644 blib/arch/auto/Parallel/MPI/Simple/Simple.bs Manifying blib/man3/Parallel::MPI::Simple.3pm [download] These warnings appear harmless enough... However make test fails as described above. Background: - using openmpi 1.4.1 which seems to run the examples ok. - ldconfig output is: vlad@bd01 Parallel-MPI-Simple-0.03]$ ldconfig -p \| grep mpi libopenmpi_malloc.so.0 (libc6,x86-64) => /usr/local/lib/libopenmpi +_malloc.so.0 libopenmpi_malloc.so (libc6,x86-64) => /usr/local/lib/libopenmpi_m +alloc.so libmpi_f90.so.0 (libc6,x86-64) => /usr/local/lib/libmpi_f90.so.0 libmpi_f90.so (libc6,x86-64) => /usr/local/lib/libmpi_f90.so libmpi_f77.so.0 (libc6,x86-64) => /usr/local/lib/libmpi_f77.so.0 libmpi_f77.so (libc6,x86-64) => /usr/local/lib/libmpi_f77.so libmpi_cxx.so.0 (libc6,x86-64) => /usr/local/lib/libmpi_cxx.so.0 libmpi_cxx.so (libc6,x86-64) => /usr/local/lib/libmpi_cxx.so libmpi.so.0 (libc6,x86-64) => /usr/local/lib/libmpi.so.0 libmpi.so (libc6,x86-64) => /usr/local/lib/libmpi.so libexempi.so.3 (libc6,x86-64) => /usr/lib64/libexempi.so.3 - libmpi.so defines the symbol openmpi_mpi_char: [[vlad@bd01 Parallel-MPI-Simple-0.03]$ objdump -tT /usr/local/lib/libm +pi.so.0 \| grep mpi_char 0000000000296920 g O .data 0000000000000200 ompi_m +pi_char 0000000000296b20 g O .data 0000000000000200 ompi_m +pi_character 0000000000296b20 g DO .data 0000000000000200 Base ompi_m +pi_character 0000000000296920 g DO .data 0000000000000200 Base ompi_m +pi_char - However the file Simple.so does not appear to look for this lib: [vlad@bd01 Parallel-MPI-Simple-0.03]$ ldd blib/arch/auto/Parallel +/MPI/Simple/Simple.so linux-vdso.so.1 => (0x00007fffaa1fe000) libc.so.6 => /lib64/libc.so.6 (0x00007fcaa1ae4000) /lib64/ld-linux-x86-64.so.2 (0x0000003da7a00000) System is FC10 x86_64 [download] What am I missing?	[reply] [d/l] [select]
Re^5: OpenMPI and Perl by Anonymous Monk on Apr 20, 2010 at 04:19 UTC
Use absolute paths, as in `-l/full/path/to/some/libmpi.so` and make sure the file appears when you do `make` (in what you've posted, the file doesn't appear).	[reply] [d/l] [select]
Re^6: OpenMPI and Perl by Vlad, the IM-perler (Novice) on Jun 15, 2010 at 00:33 UTC
Re^5: OpenMPI and Perl by Khen1950fx (Canon) on Apr 20, 2010 at 06:42 UTC
I tried it on FC6, and it installed with no problems. It seems to me that since the problem is with a shared file, you want to try a static install. The author even encourages a static install, at least for Storable. For OpenMPI, I used `./configure --disable-shared --enable-static --with-gnu-ld` [download] to configure it. I manually downloaded and installed Parallel::MPI::Simple and had no problems.	[reply] [d/l]
Re^6: OpenMPI and Perl by brunocontreras (Initiate) on Jun 16, 2011 at 13:53 UTC


No such thing as a small change
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