[petsc-users] undefined symbol: mpi_init_

Antonio Trande anto.trande at gmail.com
Mon Jun 27 04:08:00 CDT 2016 

On 06/26/2016 11:25 PM, Satish Balay wrote:
> On Sun, 26 Jun 2016, Antonio Trande wrote:
> 
>> On 06/26/2016 02:24 AM, Satish Balay wrote:
>>> On Sat, 25 Jun 2016, Antonio Trande wrote:
>>>
>>>> On 06/25/2016 09:41 PM, Antonio Trande wrote:
>>>>> On 06/25/2016 03:59 PM, Matthew Knepley wrote:
>>>>>> On Sat, Jun 25, 2016 at 8:21 AM, Antonio Trande <anto.trande at gmail.com
>>>>>> <mailto:anto.trande at gmail.com>> wrote:
>>>>>>
>>>>>>     Hi all,
>>>>>>
>>>>>>     is it possible to compile serial PETSc library ?
>>>>>>     I'm trying to compile PETSc without MPI by configuring with options:
>>>>>>
>>>>>>      --with-mpi=0 --with-mpiuni-fortran-binding=0
>>>>>>
>>>>>>     but compiler uses -I/.../petsc-3.7.2/include/petsc/mpiuni flag anyway
>>>>>>     and libpetsc.so contains an "undefined symbol":
>>>>>>
>>>>>>     undefined symbol: mpi_init_     (/usr/lib64/libpetsc.so.3.7.2)
>>>>>>
>>>>>>     How I can fix this issue ?
>>>>>>     Full log:
>>>>>>     https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/fedora-24-x86_64/00362302-petsc/build.log.gz
>>>>>>
>>>>>>
>>>>>> 1) Why are you giving --with-mpiuni-fortran-binding=0 if you still have
>>>>>> Fortran turned on? If you want to turn off Fortran, use --with-fc=0.
>>>>>
>>>>> I did't know what it does. If I active --with-mpiuni-fortran-binding,
>>>>> 'undefined symbol' disappears.
>>>>>
>>>>>>
>>>>>> 2) You did not send configure.log which is what I need, not a screen
>>>>>> capture.
>>>>>>
>>>>>> 3) I cannot see the error you sent anywhere. It would be more useful to
>>>>>> send the output from 'make test'.
>>>>>>
>>>>>>   Matt
>>>>>>  
>>>>>>
>>>>>
>>>>> I send you all config.log; petsc-serial, petsc-serial (64bit integer),
>>>>> petsc-openmpi and petsc-mpich are compiled from an own fresh source
>>>>> directory, respectively from petsc-3.7.2, build64, buildopenmpi_dir,
>>>>> buildmpich_dir.
>>>>>
>>>>> All libraries look compiled fine and related test passed.
>>>>> I will send you latest builds log from Fedora Copr build-system.
>>>>>
>>>>
>>>> No, tests not passed with
>>>>
>>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation,
>>>> probably memory access out of range
>>>>
>>>> This is a build log from Fedora 24 64 bit:
>>>> https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/fedora-24-x86_64/00362535-petsc/build.log.gz
>>>
>>>>>>>>>>>
>>> + echo 'Patch #1 (petsc-lib64.patch):'
>>> + /usr/bin/patch -p0 --fuzz=0
>>> patching file config/BuildSystem/config/setCompilers.py
>>> patching file gmakefile
>>>
>>> Patch #0 (petsc-3.7-no-rpath.patch):
>>> + /usr/bin/patch -p0 --fuzz=0
>>> patching file config/BuildSystem/config/setCompilers.py
>>> <<<<<<<<<<<
>>>
>>> Well looks like there were some modifications done to get the 'multi-variant' build working.
>>
>> Yes.
>>
>>>
>>>>>>>>>>>>>
>>> + make test -C petsc-3.7.2
>>> make: Entering directory '/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2'
>>> Running test examples to verify correct installation
>>> Using PETSC_DIR=/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2 and PETSC_ARCH=x86_64
>>> *******************Error detected during compile or link!*******************
>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>> /builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/src/snes/examples/tutorials ex19
>>> *********************************************************************************
>>> gcc -o ex19.o -c -O2 -fPIC  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fopenmp   -I/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/include -I/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/x86_64/include -I/usr/include -I/usr/include/suitesparse -I/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/include/petsc/mpiuni    `pwd`/ex19.c
>>> gcc -Wl,-z,relro  -O2 -fPIC  -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -fopenmp  -o ex19  ex19.o -L/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/x86_64/lib -L/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/x86_64/lib  -lpetsc -lmetis -L/usr/lib64 -lumfpack -lklu -lcholmod -lbtf -lccolamd -lcolamd -lcamd -lamd -lsuitesparseconfig -llapack -lblas -lOpenCL -lhwloc -lpapi -lgmp -lpthread -ljpeg -lpng -lm -L/usr/lib/gcc/x86_64-redhat-linux/6.1.1 -lgfortran -lm -lgfortran -lm -lquadmath -lm -lstdc++ -L/usr/lib/gcc/x86_64-redhat-linux/6.1.1 -ldl -lgcc_s -ldl 
>>> /usr/bin/rm -f ex19.o
>>> Possible error running C/C++ src/snes/examples/tutorials/ex19 with 1 MPI process
>>> See http://www.mcs.anl.gov/petsc/documentation/faq.html
>>> [0]PETSC ERROR: #1 PetscLogInitialize() line 219 in /builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/src/sys/logging/plog.c
>>> [0]PETSC ERROR: #2 PetscInitialize() line 891 in /builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2/src/sys/objects/pinit.c
>>> /usr/bin/sh: line 13: 16933 Aborted                 (core dumped)
>>> <<<<<<<<<<
>>>
>>> So there is no -rpath here. Which -lpetsc variant is getting used at runtime?
>>>
>>
>> Yes, no rpaths for the serial libraries, so 'libpetsc.so' and
>> 'libpetsc64.so' (renamed for mine needs).
>>
>> Test reported is for PETSc (32 bit integer) serial library: libpetsc.so
> 
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> 
> 
> + mkdir -p /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/lib64 /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/share/petsc /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/include/petsc
> + mkdir -p /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/lib64/gfortran/modules/petsc-3.7.2 /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/share/Modules/modulefiles
> + install -pm 755 x86_64/lib/libpetsc.so x86_64/lib/libpetsc.so.3.7 x86_64/lib/libpetsc.so.3.7.2 /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/lib64
> 
> + umask 022
> + cd /builddir/build/BUILD
> + cd petsc-3.7.2
> + export LD_LIBRARY_PATH=/usr/lib64:/builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/lib64
> + LD_LIBRARY_PATH=/usr/lib64:/builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/lib64
> + export PETSC_DIR=/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2
> + PETSC_DIR=/builddir/build/BUILD/petsc-3.7.2/petsc-3.7.2
> + export PETSC_ARCH=x86_64
> + PETSC_ARCH=x86_64
> + make test -C petsc-3.7.2
> 
> <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> 
> Ok - I see libpetsc.so is copied over to
> /builddir/build/BUILDROOT/petsc-3.7.2-2.fc24.x86_64/usr/lib64.  And
> this path is set in LD_LIBRARY_PATH - so the correct -lpetsc should be
> found at runtime for 'make test'
> 
> I attempted to do a build similar to what done here.
> 
>>>>>>>>>>>>>>>>>>>>
> $ cat x86_64.py 
> #!/usr/bin/python
> if __name__ == '__main__':
>   import sys
>   import os
>   sys.path.insert(0, os.path.abspath('config'))
>   import configure
>   configure_options = [
> 
>     '--prefix=/usr',
>     'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic',
>     'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic',
>     'FFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic',
>     'LDFLAGS=-Wl,-z,relro -specs=/usr/lib/rpm/redhat/redhat-hardened-ld',
>     '--with-default-arch=0',
>     '--with-make=1',
>     '--with-single-library=1',
>     '--with-precision=double',
>     '--with-petsc-arch=x86_64',
>     '--with-clanguage=C',
>     '--with-shared-libraries=1',
>     '--with-64-bit-indices=0',
>     '--with-fortran-interfaces=1',
>     '--with-windows-graphics=0',
>     '--CC=gcc',
>     '--CXX=g++',
>     '--FC=gfortran',
>     '--with-gnu-compilers=1',
>     '--with-vendor-compilers=0',
>     '--with-shared-ld=ld',
>     '--with-pic=1',
>     '--sharedLibraryFlags=',
>     '--dynamicLibraryFlags=',
>     '--with-cxx-dialect=',
>     '--with-debugging=0',
>     'COPTFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic',
>     'CXXOPTFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic',
>     'FOPTFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic -I/usr/lib64/gfortran/modules',
> 
>     '--with-blas-lib=libblas.so',
>     '--with-lapack-lib=liblapack.so',
>     '--with-blas-lapack-suffix=',
>     '--known-64-bit-blas-indices=0',
>     '--with-mpi=0',
>     '--with-mpiuni-fortran-binding=1',
>     '--with-pthread=1',
>     '--with-valgrind=1',
>     '--with-valgrind-dir=/usr',
> 
>   ]
>   configure.petsc_configure(configure_options)
> 
> <<<<<<<<<<<
> $
> 
> But I can't reprodue this error  - with the above build.. The suggestions I have for debugging are:
> 
> Somehow get the following through the build - and verify if the includes, libraries are picked up correctly
> 
> cd src/snes/examples/tutorials
> make PETSC_DIR=/home/balay/petsc PETSC_ARCH=x86_64 ex19
> ldd ex19 |grep libpetsc
> <verify the correct libpetsc.so is used>
> make PETSC_DIR=/home/balay/petsc PETSC_ARCH=x86_64 ex19.o CFLAGS=-E
> grep petscconf.h ex19.o
> <verify the correct petscconf.h is used hre>
> 
> 
> Or you could somehow try to do a minimal build - and see if the problem is reproduceable.
> [say just build 1 variant of PETSc, fewer externalpackages].

Just an additional note: changing build-system from Fedora to EPEL7
(http://fedoraproject.org/wiki/EPEL), I do not see any error:

https://copr-be.cloud.fedoraproject.org/results/sagitter/petsc/epel-7-x86_64/00362535-petsc/build.log.gz

> 
> BTW: you have:
> 
> ++ sed -e s/-D_FORTIFY_SOURCE/-D-FORTIFY-SOURCE/g
> 
> CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D-FORTIFY-SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -m64 -mtune=generic
> 
> However -Wp,-D-FORTIFY-SOURCE=2 gives me compile errors.
> 
> $ gcc -Wp,-D-FORTIFY-SOURCE=2 conftest.c
> <command-line>:0:1: error: macro names must be identifiers
> $ 
> 

Yes, PETSc's 'configure' does not like -D_FORTIFY_SOURCE (this flag
comes from default compiler flags of Fedora's '%configure' macro), I had
to change to -D-FORTIFY-SOURCE; however 'make' command uses
-D_FORTIFY_SOURCE without error.

-- 
---
Antonio Trande
mailto: sagitter 'at' fedoraproject 'dot' org
http://fedoraos.wordpress.com/
https://fedoraproject.org/wiki/User:Sagitter
GPG Key: 0x6CE6D08A
Check on https://keys.fedoraproject.org/

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