[petsc-users] When building PETSc with --prefix, reference to temporary build directory remains

[Smith, Barry F.]

  Please consider upgrading to the latest PETSc 3.11 it has many new features and fewer bugs etc.

> 5. From now on set PETSC_DIR=/readonly PETSC_ARCH=''
> step 4 moves the compiled PETSc to /readonly/ and it works, but when I compile a program with it the following line pops up in the linking command:
> -Wl,-rpath,/temporary/-Xlinker


   How are you compiling the program? 

   If you are using the PETSc make facilities the easiest fix would be to remove this offend -Wl,-rpath,/temporary/-Xlinker which isn't needed. It is likely in /readonly/lib/petsc/conf/petscvariables 

   I may have gotten the file or location wrong.  You can use find in /readonly to locate any use of -Wl,-rpath,/temporary/-Xlinker and remove them.

   Barry




> On Aug 1, 2019, at 6:07 AM, Bastian Löhrer via petsc-users <petsc-users at mcs.anl.gov> wrote:
> 
> Dear all,
> 
> I'm struggling to compile PETSc 3.3-p6 on a cluster where it is to be provided in a read-only folder.
> 
> My scenario is the following:
> PETSc shall end up in a folder into which I can write from a login node but which is read-only on compute nodes: I'll call it /readonly/ below.
> So, using a compute node, I need to compile PETSc in a different location, which I'll call /temporary/
> I have read numerous instructions on the web and here are the steps that I came up with:
> 
> 1. on a compute node: unpack the PETSc source to /temporary/ and navigate there.
> 2. configure:
> ./configure                                                                                                       \
>                  --prefix=/readonly/                                                                              \
>      --with-gnu-compilers=0                                                                                       \
>   --with-vendor-compilers=intel                                                                                   \
>      --with-large-file-io=1                                                                                       \
>                  --CFLAGS="-fPIC -L${I_MPI_ROOT}/intel64/lib -I${I_MPI_ROOT}/intel64/include -lmpi"           \
>                --CXXFLAGS="-fPIC -L${I_MPI_ROOT}/intel64/lib -I${I_MPI_ROOT}/intel64/include -lmpi -lmpicxx"  \
>                  --FFLAGS="-fPIC -L${I_MPI_ROOT}/intel64/lib -I${I_MPI_ROOT}/intel64/include -lmpi"           \
>                 --LDFLAGS="-L${I_MPI_ROOT}/intel64/lib -I${I_MPI_ROOT}/intel64/include -lmpi"                 \
>                 COPTFLAGS="-O3 -axCORE-AVX2 -xSSE4.2 -fp-model consistent -fp-model source -fp-speculation=safe -ftz"  \
>               CXXOPTFLAGS="-O3 -axCORE-AVX2 -xSSE4.2 -fp-model consistent -fp-model source -fp-speculation=safe -ftz"  \
>                 FOPTFLAGS="-O3 -axCORE-AVX2 -xSSE4.2 -fp-model consistent -fp-model source -fp-speculation=safe -ftz"  \
>    --with-blas-lapack-dir="${MKLROOT}/lib/intel64"                                                             \
>          --download-hypre                                                                                         \
>          --with-debugging=no
> 
> 3. make all
> 4. on a login node: make install
> 5. From now on set PETSC_DIR=/readonly PETSC_ARCH=''
> step 4 moves the compiled PETSc to /readonly/ and it works, but when I compile a program with it the following line pops up in the linking command:
> -Wl,-rpath,/temporary/-Xlinker
> 
> This is a problem when the drive on which /temporary/ is placed is not reachable which is the case right now due to technical issues. This causes the linking process to get stuck.
> The folder /temporary/ is to be deleted anyway so I do not see why it should be referenced here.
> 
> Am I missing something?
> 
> - Bastian