[pnetcdf-devel] [parallel-netcdf] #31: Problem installing pnetcdf on 64 bit Ubuntu machine with intel compilers

[Steve Brenner]

Wei-keng


I looked at some of the netcdf output files from my test run of the ocean model and the results are comparable to the output files sent to me by the model master, other than some minor differences which are no doubt due to running on different machines, os, and compilers.


Best regards,

Steve


Steve Brenner, Professor
Department of Geography and Environment
Bar Ilan University
Ramat Gan, Israel

Phone:       +972 3 5318973
Secretary: +972 3 531 8340
Fax:            +972 3 7384033

E-mail:       steve.brenner at biu.ac.il
Web site:    geoenv.biu.ac.il/en/Steve_Brenner



________________________________
From: Wei-keng Liao <wkliao at eecs.northwestern.edu>
Sent: Thursday, June 8, 2017 18:59
To: Steve Brenner
Cc: sbrenner at mail.biu.ac.il; parallel-netcdf at mcs.anl.gov
Subject: Re: [pnetcdf-devel] [parallel-netcdf] #31: Problem installing pnetcdf on 64 bit Ubuntu machine with intel compilers

Hi, Steve

The error you encountered is actually a bug in Makefile.in.
The file pnetcdf_pc should be in DIST_GARBAGE, not GARBAGE.
I have committed a fix to the PnetCDF repo. Below is a patch.
Thanks for your testing. Please let me know if the patch works
for you and if you have further questions.

--- Makefile.in (revision 2963)
+++ Makefile.in (working copy)
@@ -28,13 +28,14 @@
                   benchmarks \
                   examples

-GARBAGE                = pnetcdf_pc
+GARBAGE                =

 DIST_GARBAGE    = config.cache \
                   config.status \
                   config.log \
                   macros.make \
                   stamp-h \
+                  pnetcdf_pc \
                   pnetcdf.pc \
                   pnetcdf-config \
                   check_install

Wei-keng

On Jun 8, 2017, at 4:09 AM, Steve Brenner wrote:

> Wei-keng
>
> I have done a bit more digging and tried building it again but this time instead of using CC=icc CXX=icpc  FC=ifort I now used  CC=mpicc CXX=mpicxx MPIF90=mpifort which it picks up from /usr/local/bin. It now completes the build and the two tests (make check and make ptest). When I ran make install it appears to run except for the last few steps where it says
>
> rm -f pnetcdf.pc
> sed -e "s%INSTALL_PREFIX%/usr/local%g" pnetcdf_pc > pnetcdf.pc
> sed: can't read pnetcdf_pc: No such file or directory
> Makefile:147: recipe for target 'install_PKGCONFIG' failed
> make: *** [install_PKGCONFIG] Error 2
>
> When I look in /usr/local/include and /usr/local/lib the pnetcdf file are there. I will try running a test code tomorrow.
>
> Best regards
>
> Steve Brenner, Professor
> Department of Geography and Environment
> Bar Ilan University
> Ramat Gan, Israel
>
> Phone:       +972 3 5318973
> Secretary: +972 3 531 8340
> Fax:            +972 3 7384033
>
> E-mail:       steve.brenner at biu.ac.il
> Web site:    geoenv.biu.ac.il/en/Steve_Brenner
>
>
>
> From: Wei-keng Liao <wkliao at eecs.northwestern.edu>
> Sent: Thursday, June 8, 2017 10:09
> To: sbrenner at mail.biu.ac.il
> Cc: parallel-netcdf at mcs.anl.gov
> Subject: Re: [pnetcdf-devel] [parallel-netcdf] #31: Problem installing pnetcdf on 64 bit Ubuntu machine with intel compilers
>
> I do not have access to the exactly same environment, but just now built
> PnetCDF 1.8.1 on an x86_64 with Ubuntu 14.04, using mpich 3.2. built with
> icc/ifort 16.0.3 and 17.0.2. The build was successful.
>
> If the build hung at the compile time, then I would guess it most likely
> is an issue of the compiler. Can check your MPI fortran compiler to
> make sure it compiles other F90 programs without problems.
>
> Wei-keng
>
> On Jun 8, 2017, at 12:48 AM, parallel-netcdf wrote:
>
> > #31: Problem installing pnetcdf on 64 bit Ubuntu machine with intel compilers
> > -------------------------------------+--------------------------------------
> > Reporter:  sbrenner@…               |       Owner:  robl
> >     Type:  defect/bug               |      Status:  new
> > Priority:  major                    |   Milestone:
> > Component:  parallel-netcdf          |     Version:  1.8.1
> > Keywords:                           |
> > -------------------------------------+--------------------------------------
> > I am trying to install pnetcdf on a i7 machine running Ubuntu linux 16.04
> > with the intel 2017 c, c++ and fortran compliers. It configues ok but in
> > the make step it hangs when trying to compile pnetcdf.f90 (no error is
> > returned, it simple is stuck in the compilation step). I have tried both
> > versions 1.8.1 and 1.7.0. Any suggestions?
> >
> > --
> > Ticket URL: <http://trac.mcs.anl.gov/projects/parallel-netcdf/ticket/31>
> > parallel-netcdf <https://trac.mcs.anl.gov/projects/parallel-netcdf>
Parallel netCDF: A Parallel I/O Library for NetCDF File Access<https://trac.mcs.anl.gov/projects/parallel-netcdf>
trac.mcs.anl.gov
Parallel netCDF: A Parallel I/O Library for NetCDF File Access. Parallel netCDF (PnetCDF) is jointly developed by Northwestern University and Argonne National Laboratory.


> Parallel netCDF: A Parallel I/O Library for NetCDF File Access
> trac.mcs.anl.gov
> Parallel netCDF: A Parallel I/O Library for NetCDF File Access. Parallel netCDF (PnetCDF) is jointly developed by Northwestern University and Argonne National Laboratory.
>
> >
> > _______________________________________________
> > pnetcdf-devel mailing list
> > pnetcdf-devel at lists.mcs.anl.gov
> > https://lists.mcs.anl.gov/mailman/listinfo/pnetcdf-devel
>

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