<div dir="ltr">Dear Professor Roman,<div><br></div><div>I decided to install petsc-3.10.3 with slepc since I did it once succesfully. Thanks for your help.</div><div><br></div><div>Eda</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Jose E. Roman <<a href="mailto:jroman@dsic.upv.es">jroman@dsic.upv.es</a>>, 19 Mar 2019 Sal, 15:15 tarihinde şunu yazdı:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">What is the output of 'make check' in $PETSC_DIR ?<br>
<br>
> El 19 mar 2019, a las 13:02, Eda Oktay <<a href="mailto:eda.oktay@metu.edu.tr" target="_blank">eda.oktay@metu.edu.tr</a>> escribió:<br>
> <br>
> Without slepc, I configured petsc succesfully. Then I installed slepc with following steps:<br>
> <br>
> export PETSC_ARCH=arch-linux2-c-debug<br>
> export PETSC_DIR=/home/slurm_local/e200781/petsc-3.10.4<br>
> export SLEPC_DIR=/home/slurm_local/e200781/slepc-3.10.2<br>
> cd slepc-3.10.2<br>
> ./configure<br>
> <br>
> However, I still get the error:<br>
> <br>
> Checking environment... done<br>
> Checking PETSc installation... <br>
> ERROR: Unable to link with PETSc<br>
> ERROR: See "arch-linux2-c-debug/lib/slepc/conf/configure.log" file for details<br>
> <br>
> Where the configure.log is:<br>
> <br>
> ================================================================================<br>
> Starting Configure Run at Tue Mar 19 14:57:21 2019<br>
> Configure Options: <br>
> Working directory: /home/slurm_local/e200781/slepc-3.10.2<br>
> Python version:<br>
> 2.7.9 (default, Sep 25 2018, 20:42:16) <br>
> [GCC 4.9.2]<br>
> make: /usr/bin/make<br>
> PETSc source directory: /home/slurm_local/e200781/petsc-3.10.4<br>
> PETSc install directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug<br>
> PETSc version: 3.10.4<br>
> PETSc architecture: arch-linux2-c-debug<br>
> SLEPc source directory: /home/slurm_local/e200781/slepc-3.10.2<br>
> SLEPc version: 3.10.2<br>
> ================================================================================<br>
> Checking PETSc installation...<br>
> #include "petscsnes.h"<br>
> int main() {<br>
> Vec v; Mat m; KSP k;<br>
> PetscInitializeNoArguments();<br>
> VecCreate(PETSC_COMM_WORLD,&v);<br>
> MatCreate(PETSC_COMM_WORLD,&m);<br>
> KSPCreate(PETSC_COMM_WORLD,&k);<br>
> return 0;<br>
> }<br>
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -o checklink.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3 -I/home/slurm_local/e200781/petsc-3.10.4/include -I/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/include `pwd`/checklink.c<br>
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3 -o checklink checklink.o -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -lopenblas -lparmetis -lmetis -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl<br>
> /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40<br>
> /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40<br>
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningParmetisSetRepartition'<br>
> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningCreate_Parmetis'<br>
> collect2: error: ld returned 1 exit status<br>
> makefile:2: recipe for target 'checklink' failed<br>
> make: *** [checklink] Error 1<br>
> <br>
> ERROR: Unable to link with PETSc<br>
> <br>
> Jose E. Roman <<a href="mailto:jroman@dsic.upv.es" target="_blank">jroman@dsic.upv.es</a>>, 19 Mar 2019 Sal, 14:08 tarihinde şunu yazdı:<br>
> There seems to be a link problem with PETSc.<br>
> Suggest re-configuring without the option --download-slepc<br>
> Then, after building PETSc, try 'make check' to make sure that PETSc is built correctly. Then install SLEPc afterwards.<br>
> Jose<br>
> <br>
> <br>
> > El 19 mar 2019, a las 11:58, Eda Oktay <<a href="mailto:eda.oktay@metu.edu.tr" target="_blank">eda.oktay@metu.edu.tr</a>> escribió:<br>
> > <br>
> > ================================================================================<br>
> > Starting Configure Run at Tue Mar 19 11:53:05 2019<br>
> > Configure Options: --prefix=/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug<br>
> > Working directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/externalpackages/git.slepc<br>
> > Python version:<br>
> > 2.7.9 (default, Sep 25 2018, 20:42:16) <br>
> > [GCC 4.9.2]<br>
> > make: /usr/bin/make<br>
> > PETSc source directory: /home/slurm_local/e200781/petsc-3.10.4<br>
> > PETSc install directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug<br>
> > PETSc version: 3.10.4<br>
> > PETSc architecture: arch-linux2-c-debug<br>
> > SLEPc source directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/externalpackages/git.slepc<br>
> > SLEPc install directory: /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug<br>
> > SLEPc version: 3.10.1<br>
> > ================================================================================<br>
> > Checking PETSc installation...<br>
> > #include "petscsnes.h"<br>
> > int main() {<br>
> > Vec v; Mat m; KSP k;<br>
> > PetscInitializeNoArguments();<br>
> > VecCreate(PETSC_COMM_WORLD,&v);<br>
> > MatCreate(PETSC_COMM_WORLD,&m);<br>
> > KSPCreate(PETSC_COMM_WORLD,&k);<br>
> > return 0;<br>
> > }<br>
> > make[2]: Entering directory '/tmp/slepc-2F1MtJ'<br>
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -o checklink.o -c -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3 -I/home/slurm_local/e200781/petsc-3.10.4/include -I/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/include `pwd`/checklink.c<br>
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/bin/mpicc -fPIC -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -fvisibility=hidden -g3 -o checklink checklink.o -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -L/home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9 -L/usr/lib/gcc/x86_64-linux-gnu/4.9 -Wl,-rpath,/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu -L/lib/x86_64-linux-gnu -lpetsc -lopenblas -lparmetis -lmetis -lm -lX11 -lstdc++ -ldl -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm -lgfortran -lm -lgcc_s -lquadmath -lpthread -lstdc++ -ldl<br>
> > /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40<br>
> > /usr/bin/ld: warning: libmpi.so.0, needed by /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libopenblas.so, may conflict with libmpi.so.40<br>
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningParmetisSetRepartition'<br>
> > /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/libpetsc.so: undefined reference to `MatPartitioningCreate_Parmetis'<br>
> > collect2: error: ld returned 1 exit status<br>
> > makefile:2: recipe for target 'checklink' failed<br>
> > make[2]: *** [checklink] Error 1<br>
> > make[2]: Leaving directory '/tmp/slepc-2F1MtJ'<br>
> > <br>
> > ERROR: Unable to link with PETSc<br>
> > <br>
> > <br>
> > Jose E. Roman <<a href="mailto:jroman@dsic.upv.es" target="_blank">jroman@dsic.upv.es</a>>, 19 Mar 2019 Sal, 13:49 tarihinde şunu yazdı:<br>
> > Correction: the correct path is $PETSC_DIR/$PETSC_ARCH/externalpackages/git.slepc/$PETSC_ARCH/lib/slepc/conf/configure.log<br>
> > <br>
> > <br>
> > <br>
> > > El 19 mar 2019, a las 11:46, Jose E. Roman via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> escribió:<br>
> > > <br>
> > > And what is in $SLEPC_DIR/arch-linux2-c-debug/lib/slepc/conf/configure.log ?<br>
> > > Jose<br>
> > > <br>
> > >> El 19 mar 2019, a las 11:41, Eda Oktay via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> escribió:<br>
> > >> <br>
> > >> This is slepc.log:<br>
> > >> <br>
> > >> Checking environment... done<br>
> > >> Checking PETSc installation... <br>
> > >> ERROR: Unable to link with PETSc<br>
> > >> ERROR: See "arch-linux2-c-debug/lib/slepc/conf/configure.log" file for details<br>
> > >> <br>
> > >> <br>
> > >> <br>
> > >> Matthew Knepley <<a href="mailto:knepley@gmail.com" target="_blank">knepley@gmail.com</a>>, 19 Mar 2019 Sal, 13:36 tarihinde şunu yazdı:<br>
> > >> On Tue, Mar 19, 2019 at 6:31 AM Eda Oktay via petsc-users <<a href="mailto:petsc-users@mcs.anl.gov" target="_blank">petsc-users@mcs.anl.gov</a>> wrote:<br>
> > >> Hello,<br>
> > >> <br>
> > >> I am trying to install PETSc with following configure options:<br>
> > >> <br>
> > >> ./configure --download-openmpi --download-openblas --download-slepc --download-cmake --download-metis --download-parmetis<br>
> > >> <br>
> > >> Compilation is done but after the following command, I got an error:<br>
> > >> <br>
> > >> make PETSC_DIR=/home/slurm_local/e200781/petsc-3.10.4 PETSC_ARCH=arch-linux2-c-debug all<br>
> > >> <br>
> > >> *** Building slepc ***<br>
> > >> **************************ERROR*************************************<br>
> > >> Error building slepc. Check arch-linux2-c-debug/lib/petsc/conf/slepc.log<br>
> > >> <br>
> > >> We need slepc.log<br>
> > >> <br>
> > >> Thanks,<br>
> > >> <br>
> > >> Matt<br>
> > >> <br>
> > >> ********************************************************************<br>
> > >> /home/slurm_local/e200781/petsc-3.10.4/arch-linux2-c-debug/lib/petsc/conf/petscrules:46: recipe for target 'slepcbuild' failed<br>
> > >> make[1]: *** [slepcbuild] Error 1<br>
> > >> make[1]: Leaving directory '/home/slurm_local/e200781/petsc-3.10.4'<br>
> > >> **************************ERROR*************************************<br>
> > >> Error during compile, check arch-linux2-c-debug/lib/petsc/conf/make.log<br>
> > >> Send it and arch-linux2-c-debug/lib/petsc/conf/configure.log to <a href="mailto:petsc-maint@mcs.anl.gov" target="_blank">petsc-maint@mcs.anl.gov</a><br>
> > >> ********************************************************************<br>
> > >> makefile:30: recipe for target 'all' failed<br>
> > >> make: *** [all] Error 1<br>
> > >> <br>
> > >> How can I fix the problem?<br>
> > >> <br>
> > >> Thank you,<br>
> > >> <br>
> > >> Eda<br>
> > >> <br>
> > >> <br>
> > >> -- <br>
> > >> What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
> > >> -- Norbert Wiener<br>
> > >> <br>
> > >> <a href="https://www.cse.buffalo.edu/~knepley/" rel="noreferrer" target="_blank">https://www.cse.buffalo.edu/~knepley/</a><br>
> > > <br>
> > <br>
> <br>
<br>
</blockquote></div>