[petsc-users] Errors while install pets-dev

(Rebecca) Xuefei YUAN xy2102 at columbia.edu
Mon Jan 25 23:03:00 CST 2010 

Dear Satish,

Yes, I do have problems with external packages, so I downloaded them  
manually and move them into petsc-dev.

So the configure has options like

rebecca at YuanWork:~/soft/petsc-dev$ ./config/configure.py --with-cc=gcc  
--with-fc=gfortran  
--download-f-blas-lapack=/home/rebecca/soft/petsc-dev/fblaslapack-3.1.1.tar.gz  
--download-mpich=/home/rebecca/soft/petsc-dev/mpich2-1.2.1.tar.gz   
--download-sowing=/home/rebecca/soft/petsc-dev/sowing-1.1.15.tar.gz  
--download-c2html=/home/rebecca/soft/petsc-dev/c2html.tar.gz

The Fortran compiler I have is g77 and gfortran.

If I do not use Fortran, will this be fine?

Cheers,

Rebecca

Quoting Satish Balay <balay at mcs.anl.gov>:

> Ok - is your manual install '2.  access tarballs directly from our
> mercurial server.?
> http://www.mcs.anl.gov/petsc/petsc-as/developers/index.html
>
>
> And do you have problem with --download-pacakge options due to the
> proxy issues? If so - that might explain the problem.
>
> petsc-dev - with 'hg' - or with 'tarballs from mercurial' server
> require sowing package for the fortran interface. If configure is
> unable to install sowing - then fortran interface is not generated.
>
> Thus unresolved symbol errors when compiling fortran examples.
>
> This can be verified by looking at configure.log and make.log for this
> build.
>
> Satish
>
>
> On Mon, 25 Jan 2010, Satish Balay wrote:
>
>>
>> On Mon, 25 Jan 2010, (Rebecca) Xuefei YUAN wrote:
>>
>> > Dear Satish,
>> >
>> > I switched to install it manually
>>
>> What do you mean? Did you get the nightly tarball?
>>
>> > and encounter an error when "make test".
>>
>> Did the build go through fine without errors??
>>
>> Send over configure.log and make.log to petsc-maint.
>>
>> Satish
>>
>> > Here are error messages:
>> >
>> > Completed building libraries
>> > =========================================
>> > Now to check if the libraries are working do: make test
>> > =========================================
>> > rebecca at YuanWork:~/soft/petsc-dev$ make test
>> > Running test examples to verify correct installation
>> > C/C++ example src/snes/examples/tutorials/ex19 run successfully with 1 MPI
>> > process
>> > C/C++ example src/snes/examples/tutorials/ex19 run successfully with 2 MPI
>> > processes
>> > --------------Error detected during compile or   
>> link!-----------------------
>> > See   
>> http://www.mcs.anl.gov/petsc/petsc-2/documentation/troubleshooting.html
>> > /home/rebecca/soft/petsc-dev/linux-gnu-c-debug/bin/mpif90 -c  -Wall
>> > -Wno-unused-variable -g
>> > -I/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/include
>> > -I/home/rebecca/soft/petsc-dev/include
>> > -I/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/include
>> > -I/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/include
>> > -I/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/include    -o   
>> ex5f.o ex5f.F
>> > /home/rebecca/soft/petsc-dev/linux-gnu-c-debug/bin/mpif90 -Wall
>> > -Wno-unused-variable -g  -o ex5f ex5f.o
>> > -Wl,-rpath,/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/lib
>> > -L/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/lib -lpetscsnes   
>> -lpetscksp
>> > -lpetscdm -lpetscmat -lpetscvec -lpetsc   -lX11
>> > -Wl,-rpath,/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/lib
>> > -L/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/lib -lflapack   
>> -lfblas -lnsl
>> > -lrt -lm -L/home/rebecca/soft/petsc-dev/linux-gnu-c-debug/lib
>> > -L/usr/lib/gcc/i486-linux-gnu/4.2.4 -ldl -lmpich -lopa -lpthread   
>> -lrt -lgcc_s
>> > -lmpichf90 -lgfortran -lm -lm -ldl -lmpich -lopa -lpthread -lrt   
>> -lgcc_s -ldl
>> > ex5f.o: In function `MAIN__':
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:103:   
>> undefined
>> > reference to `snescreate_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:120:   
>> undefined
>> > reference to `dacreateglobalvector_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:121:   
>> undefined
>> > reference to `vecduplicate_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:131:   
>> undefined
>> > reference to `dagetcorners_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:133:   
>> undefined
>> > reference to `dagetghostcorners_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:211:   
>> undefined
>> > reference to `snessetfromoptions_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:223:   
>> undefined
>> > reference to `snesgetiterationnumber_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:235:   
>> undefined
>> > reference to `matdestroy_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:236:   
>> undefined
>> > reference to `matdestroy_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:237:   
>> undefined
>> > reference to `vecdestroy_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:238:   
>> undefined
>> > reference to `vecdestroy_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:239:   
>> undefined
>> > reference to `snesdestroy_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:240:   
>> undefined
>> > reference to `dadestroy_'
>> > ex5f.o: In function `forminitialguess_':
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:286:   
>> undefined
>> > reference to `dmgetlocalvector_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:299:   
>> undefined
>> > reference to `dalocaltoglobal_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:300:   
>> undefined
>> > reference to `dmrestorelocalvector_'
>> > ex5f.o: In function `formjacobianlocal_':
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:523:   
>> undefined
>> > reference to `matsetvalueslocal_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:538:   
>> undefined
>> > reference to `matsetvalueslocal_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:542:   
>> undefined
>> > reference to `matassemblybegin_'
>> >   
>> /home/rebecca/soft/petsc-dev/src/snes/examples/tutorials/ex5f.F:543:   
>> undefined
>> > reference to `matassemblyend_'
>> > collect2: ld returned 1 exit status
>> > make[3]: [ex5f] Error 1 (ignored)
>> > /bin/rm -f ex5f.o
>> > Completed test examples
>> >
>> > What could possibly wrong?
>> >
>> > Thanks!
>> >
>> > Rebecca
>> >
>> >
>> >
>> >
>> > Quoting Satish Balay <balay at mcs.anl.gov>:
>> >
>> > > Sorry - forgot to mention the url
>> > >
>> > >   
>> http://mail.openjdk.java.net/pipermail/build-dev/2007-December/000628.html
>> > >
>> > > Satish
>> > >
>> > > On Mon, 25 Jan 2010, Satish Balay wrote:
>> > >
>> > > > Do you have to use proxy for your http connections? If so - perhaps
>> > > > you can try adding the settings to ~/.hgrc - as this url indicates and
>> > > > see if it fixes the problem.
>> > > >
>> > > > Satish
>> > > >
>> > > > On Mon, 25 Jan 2010, (Rebecca) Xuefei YUAN wrote:
>> > > >
>> > > > > Hi,All,
>> > > > >
>> > > > > I try to install a pets-dev locally according to the instruction
>> > > > >
>> > > > > http://www.mcs.anl.gov/petsc/petsc-as/developers/index.html
>> > > > >
>> > > > > I have installed mercurial, but when I get the second step,  
>>  I get  some
>> > > > > error
>> > > > > like:
>> > > > >
>> > > > > rebecca at YuanWork:~/soft$ hg clone
>> > > > > http://petsc.cs.iit.edu/petsc/petsc-dev
>> > > > > destination directory: petsc-dev
>> > > > > abort: error: Name or service not known
>> > > > >
>> > > > > Is there anything wrong?
>> > > > >
>> > > > > Thanks!
>> > > > >
>> > > > >
>> > > >
>> > > >
>> > >
>> > >
>> > >
>> >
>> >
>> >
>> >
>>
>>
>
>
>



-- 
(Rebecca) Xuefei YUAN
Department of Applied Physics and Applied Mathematics
Columbia University
Tel:917-399-8032
www.columbia.edu/~xy2102

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