[petsc-dev] [petsc-users] Error during PETSc build on Edison

[Amneet Bhalla]

P.S: I was also mucking with cray-petsc. However, I could not use it in my
application. Cray-petsc is built with
parallel hdf5 and some of the libraries I need use serial hdf5. At runtime,
the application picks parallel hdf5
and the application crashes :-(. I tried this on my laptop also and got the
same result.

I think the only way out is to build my own version of PETSc without
(parallel) hdf5.

On Thu, Feb 1, 2018 at 7:52 AM, Amneet Bhalla <mail2amneet at gmail.com> wrote:

> OK, I am now trying with INTEL compilers (as the GNU didn't seem to run
> the snes example manually).
> Now I am getting error with fortran and C++ linkage. See the configure.log
>
>
>
> On Mon, Jan 29, 2018 at 9:13 PM, Smith, Barry F. <bsmith at mcs.anl.gov>
> wrote:
>
>>
>>
>> > On Jan 29, 2018, at 11:11 PM, Amneet Bhalla <mail2amneet at gmail.com>
>> wrote:
>> >
>> > I see. It compiled and linked on the frontend quickly. although with a
>> warning
>> > /global/homes/a/apbhalla/softwares/PETSc-BitBucket/PETSc/
>> linux-opt/lib/libpetsc.a(send.o): In function `PetscOpenSocket':
>> > send.c:(.text+0x346): warning: Using 'gethostbyname' in statically
>> linked applications requires at runtime the shared libraries from the glibc
>> version used for linking
>> > /usr/bin/rm -f ex3.o
>>
>>   Sadly this message will still be there long after we are all dead,
>> assuming Cray is still in business.
>>
>> >
>> > Not sure how to get rid of this.
>> >
>> > However, the executable is stuck in the interactive session.  I wonder
>> if something is up with the interactive session itself.
>> > I am using the command salloc -N 1 -q debug -L SCRATCH
>> > to create one, and running the example is
>> >
>> > apbhalla at nid00108:~/softwares/PETSc-BitBucket/PETSc/src/snes/examples/tutorials$
>> srun -n 3 ./ex3
>> >
>> >
>> > On Mon, Jan 29, 2018 at 9:01 PM, Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> > You should be able to compile/link on the frontend - and then run on
>> the interactive node.
>> >
>> > Satish
>> >
>> > On Tue, 30 Jan 2018, Amneet Bhalla wrote:
>> >
>> > > It's way too long. The interactive session expired :-(. I think the
>> default
>> > > time is ~30 minutes.
>> > > I will let it link in a new session and see if that works.
>> > >
>> > > On Mon, Jan 29, 2018 at 8:55 PM, Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> > >
>> > > > On Tue, 30 Jan 2018, Amneet Bhalla wrote:
>> > > >
>> > > > > The configure and build worked. When I do make test, it asks to
>> run
>> > > > > snes examples manually as nersc does not
>> > > > > provide mpiexec command. I tried an interactive session and tried
>> > > > building
>> > > > > snes/examples/tutorials/ex3
>> > > > >
>> > > > > % make VERBOSE=1 ex3
>> > > > >
>> > > > > I am getting stuck at
>> > > >
>> > > > Perhaps its taking a long time to link - and you need to wait for
>> it [to
>> > > > complete]?
>> > > >
>> > > > Satish
>> > > > >
>> > > > > apbhalla at nid03377:
>> > > > > ~/softwares/PETSc-BitBucket/PETSc/src/snes/examples/tutorials$
>> make
>> > > > > VERBOSE=1 ex3
>> > > > >
>> > > > > cc -O3  -o ex3 ex3.o
>> > > > > -L/global/homes/a/apbhalla/softwares/PETSc-BitBucket/PETSc/
>> linux-opt/lib
>> > > > > -Wl,-rpath,/global/homes/a/apbhalla/softwares/PETSc-
>> > > > BitBucket/PETSc/linux-opt/lib
>> > > > > -lpetsc -lHYPRE -ldl -lstdc++
>> > > > >
>> > > > > I am not sure what's going on as there is no return after that.
>> > > > >
>> > > > > On Mon, Jan 29, 2018 at 8:27 PM, Satish Balay <balay at mcs.anl.gov>
>> wrote:
>> > > > >
>> > > > > > On Tue, 30 Jan 2018, Smith, Barry F. wrote:
>> > > > > >
>> > > > > > >    Master now should not require this horrible flags. Could
>> you do a
>> > > > > > > test build with master on edison without these flags and see
>> what
>> > > > > > > happens?
>> > > > > >
>> > > > > > It does not work. Will move this thread (with logs) to
>> petsc-maint.
>> > > > > >
>> > > > > > Satish
>> > > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > > >
>> > > >
>> > > >
>> > >
>> > >
>> > >
>> >
>> >
>> >
>> >
>> > --
>> > --Amneet
>> >
>> >
>> >
>>
>>
>
>
> --
> --Amneet
>
>
>
>


-- 
--Amneet
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