[petsc-users] Errors while install pets-dev

[Satish Balay]

The fortran stubs should have been generated with
--download-sowing=/home/rebecca/soft/petsc-dev/sowing-1.1.15.tar.gz

But - if you don't use fortran - you can ignore fortran errors - or
simply use '--with-fc=0' [unless you need an externalpackage that need
fortran. For blas you can use --download-c-blas-lapack]

Satish

On Tue, 26 Jan 2010, (Rebecca) Xuefei YUAN wrote:

> 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!
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > > >
> > > > 
> > > > 
> > > > 
> > > > 
> > > 
> > > 
> > 
> > 
> > 
> 
> 
> 
>