Thread: [Libmesh-users] how to compile with installed netcdf?

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libmesh-users

[Libmesh-users] how to compile with installed netcdf?

From: <ed...@op...> - 2019-12-25 13:41:27

Hello,

Is there a way to use my system's netcdf instead of the one in the 
contrib directory? Thanks!

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Re: [Libmesh-users] how to compile with installed netcdf?

From: <ed...@op...> - 2019-12-30 00:22:07

I attach a patch for netcdf.m4 which can help to use the system's 
netcdf. Mind you, this is the first autoconf script that I prepare. 
=make= is currently running. If there is a better solution, let me know. 
You can also find the file here:
https://notabug.org/broncodev/libmesh-pkgbuild and you need to run 
=autoconf= in the libmesh root directory

On 2019-12-25 13:40, ed...@op... wrote:
> Hello,
> 
> Is there a way to use my system's netcdf instead of the one in the
> contrib directory? Thanks!

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Re: [Libmesh-users] how to compile with installed netcdf?

From: <ed...@op...> - 2019-12-30 10:41:13

Attachments: PKGBUILD

I can still not compile with my system's netcdf. With this code, I can 
compile and run a test:

   #+begin_SRC cpp
     #include "netcdf.h"

     int main(void){
              static int ncid;
              nc_create("test.nc", NC_NETCDF4|NC_CLOBBER, &ncid);}
   #+end_SRC

   #+begin_SRC bash
     gcc -Wall -lnetcdf -L/usr/lib -I/usr/include -o run-test test.cpp
     ./run-test
     ls test.nc
   #+end_SRC

   #+RESULTS:
   : test.nc

I added what I thought would be the same to netcdf.m4, but it seems that 
it cannot compile. I show the relevant portions of the attached file

   #+begin_SRC autoconf
     m4_define([_AX_CXX_COMPILE_NETCDF_preamble],
     [[
     @%:@include "netcdf.h"
     ]])

     m4_define([_AX_CXX_COMPILE_NETCDF_body],
     [[
     static int ncid;
     nc_create("test.nc", NC_NETCDF4|NC_CLOBBER, &ncid);
     ]])
   #+END_SRC

This message does not show up in the log

   #+begin_SRC autoconf
     AS_IF([test "$netcdfincFound" = "no"],
     [
     AC_MSG_RESULT(NETCDF header files not found!)
     enablenetcdf=no;
     ])
   #+end_SRC

So I think that this should work

   #+BEGIN_SRC autoconf
     NETCDF_INCLUDE="-I$NETCDF_INC"
   #+END_SRC
---8<--- snip
   #+begin_SRC autoconf
     AS_IF([test "x$RPATHFLAG" != "x" && test -d $NETCDF_LIB],
           [NETCDF_RPATH_FLAGS="${RPATHFLAG}${NETCDF_LIB}"
            NETCDF_LIBRARY="${RPATHFLAG}${NETCDF_LIB} $NETCDF_LIBRARY"
           ],
           [NETCDF_LIBRARY="-L${NETCDF_LIB} -lnetcdf $NETCDF_LIBRARY"])
     LIBS="$LIBS $NETCDF_LIBRARY"
     CPPFLAGS="$CPPFLAGS $NETCDF_INCLUDE"
   #+end_SRC

But I get the error from here

   #+begin_SRC autoconf
     
AC_LINK_IFELSE([AC_LANG_PROGRAM([_AX_CXX_COMPILE_NETCDF_preamble],[_AX_CXX_COMPILE_NETCDF_body])],
     [AC_DEFINE(HAVE_NETCDF, 1, [Flag indicating whether the library will 
be compiled with Netcdf support])],
     [AC_MSG_ERROR(*** Linking a test program against the NETCDF 
libraries failed)])
   #+end_SRC

What I find funny is that if I force

   #+begin_SRC autoconf
     LIBS="$LIBS -lnetcdf -L/usr/lib"
     CPPFLAGS="$CPPFLAGS -I/usr/include"
   #+end_SRC

then, configure runs well, but still picks up the =contrib/netcdf4=. I 
think that I will live with this. I am sure that there is a silly 
mistake. I hope that it is useful to others. If you want more debugging 
information, let me know.

On 2019-12-30 00:21, ed...@op... wrote:
> I attach a patch for netcdf.m4 which can help to use the system's
> netcdf. Mind you, this is the first autoconf script that I prepare.
> =make= is currently running. If there is a better solution, let me
> know. You can also find the file here:
> https://notabug.org/broncodev/libmesh-pkgbuild and you need to run
> =autoconf= in the libmesh root directory
> 
> On 2019-12-25 13:40, ed...@op... wrote:
>> Hello,
>> 
>> Is there a way to use my system's netcdf instead of the one in the
>> contrib directory? Thanks!
> 
> 
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Re: [Libmesh-users] how to compile with installed netcdf?

From: <ed...@op...> - 2019-12-30 14:34:06

I think that I found a way to use my system's netcdf with libMesh (make 
check gave no errors).

- System: Parabola GNU/Linux x86_64 AMD Ryzen 2500
- PETSc from Git commit 5f77d1e0e5
- libMesh from Git commit 19706028f
- a bunch of packagees from repositories (cgns 3.4.0-2, hdf5-openmpi 
1.10.5-1, hdf5-openmpi 1.10.5-1, netcdf-openmpi 4.7.1-2, paraview 
5.7.0-3, pnetcdf-openmpi 1.12.0-1, python-h5py-openmpi 2.10.0-1, vtk 
8.2.0-9, hwloc 2.1.0-2, metis 5.1.0.p7-1, openmp 9.0.0-2, openmpi 
4.0.2-3, suitesparse 5.6.0-1, scotch 6.0.6-1)
- some from AUR's user-contributed packages (fftw-mpi 3.3.8-1, hypre-sm 
2.14.0-1, mumps 5.2.1-3, superlu 5.2.1-9)

If you want to try, my recipe is here:
https://notabug.org/broncodev/libmesh-pkgbuild.git (commit e3d46fc)
https://notabug.org/broncodev/petsc-pkgbuild.git (commit 3e9d679)

MUMPS is still not detected by libMesh :( .
Let me know if I did something unwise. Thanks!


On 2019-12-30 10:40, ed...@op... wrote:
> I can still not compile with my system's netcdf. With this code, I can
> compile and run a test:
> 
>   #+begin_SRC cpp
>     #include "netcdf.h"
> 
>     int main(void){
>              static int ncid;
>              nc_create("test.nc", NC_NETCDF4|NC_CLOBBER, &ncid);}
>   #+end_SRC
> 
>   #+begin_SRC bash
>     gcc -Wall -lnetcdf -L/usr/lib -I/usr/include -o run-test test.cpp
>     ./run-test
>     ls test.nc
>   #+end_SRC
> 
>   #+RESULTS:
>   : test.nc
> 
> I added what I thought would be the same to netcdf.m4, but it seems
> that it cannot compile. I show the relevant portions of the attached
> file
> 
>   #+begin_SRC autoconf
>     m4_define([_AX_CXX_COMPILE_NETCDF_preamble],
>     [[
>     @%:@include "netcdf.h"
>     ]])
> 
>     m4_define([_AX_CXX_COMPILE_NETCDF_body],
>     [[
>     static int ncid;
>     nc_create("test.nc", NC_NETCDF4|NC_CLOBBER, &ncid);
>     ]])
>   #+END_SRC
> 
> This message does not show up in the log
> 
>   #+begin_SRC autoconf
>     AS_IF([test "$netcdfincFound" = "no"],
>     [
>     AC_MSG_RESULT(NETCDF header files not found!)
>     enablenetcdf=no;
>     ])
>   #+end_SRC
> 
> So I think that this should work
> 
>   #+BEGIN_SRC autoconf
>     NETCDF_INCLUDE="-I$NETCDF_INC"
>   #+END_SRC
> ---8<--- snip
>   #+begin_SRC autoconf
>     AS_IF([test "x$RPATHFLAG" != "x" && test -d $NETCDF_LIB],
>           [NETCDF_RPATH_FLAGS="${RPATHFLAG}${NETCDF_LIB}"
>            NETCDF_LIBRARY="${RPATHFLAG}${NETCDF_LIB} $NETCDF_LIBRARY"
>           ],
>           [NETCDF_LIBRARY="-L${NETCDF_LIB} -lnetcdf $NETCDF_LIBRARY"])
>     LIBS="$LIBS $NETCDF_LIBRARY"
>     CPPFLAGS="$CPPFLAGS $NETCDF_INCLUDE"
>   #+end_SRC
> 
> But I get the error from here
> 
>   #+begin_SRC autoconf
> 
> AC_LINK_IFELSE([AC_LANG_PROGRAM([_AX_CXX_COMPILE_NETCDF_preamble],[_AX_CXX_COMPILE_NETCDF_body])],
>     [AC_DEFINE(HAVE_NETCDF, 1, [Flag indicating whether the library
> will be compiled with Netcdf support])],
>     [AC_MSG_ERROR(*** Linking a test program against the NETCDF
> libraries failed)])
>   #+end_SRC
> 
> What I find funny is that if I force
> 
>   #+begin_SRC autoconf
>     LIBS="$LIBS -lnetcdf -L/usr/lib"
>     CPPFLAGS="$CPPFLAGS -I/usr/include"
>   #+end_SRC
> 
> then, configure runs well, but still picks up the =contrib/netcdf4=. I
> think that I will live with this. I am sure that there is a silly
> mistake. I hope that it is useful to others. If you want more
> debugging information, let me know.
> 
> On 2019-12-30 00:21, ed...@op... wrote:
>> I attach a patch for netcdf.m4 which can help to use the system's
>> netcdf. Mind you, this is the first autoconf script that I prepare.
>> =make= is currently running. If there is a better solution, let me
>> know. You can also find the file here:
>> https://notabug.org/broncodev/libmesh-pkgbuild and you need to run
>> =autoconf= in the libmesh root directory
>> 
>> On 2019-12-25 13:40, ed...@op... wrote:
>>> Hello,
>>> 
>>> Is there a way to use my system's netcdf instead of the one in the
>>> contrib directory? Thanks!
>> 
>> 
>> -------------------------------------------------
>> This free account was provided by VFEmail.net - report spam to 
>> ab...@vf...
>> 
>> ONLY AT VFEmail! - Use our Metadata Mitigator to keep your email out
>> of the NSA's hands!
>> $24.95 ONETIME Lifetime accounts with Privacy Features!  15GB disk! No
>> bandwidth quotas!
>> Commercial and Bulk Mail Options!
>> _______________________________________________
>> Libmesh-users mailing list
>> Lib...@li...
>> https://lists.sourceforge.net/lists/listinfo/libmesh-users
> 
> 
> -------------------------------------------------
> This free account was provided by VFEmail.net - report spam to 
> ab...@vf...
> 
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> of the NSA's hands!
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> bandwidth quotas!
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> _______________________________________________
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> Lib...@li...
> https://lists.sourceforge.net/lists/listinfo/libmesh-users

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Re: [Libmesh-users] how to compile with installed netcdf?

From: Stogner, R. H <roy...@ic...> - 2019-12-30 17:27:24

On Mon, 30 Dec 2019, ed...@op... wrote:

> I think that I found a way to use my system's netcdf with libMesh (make check 
> gave no errors).
>
> - System: Parabola GNU/Linux x86_64 AMD Ryzen 2500
> - PETSc from Git commit 5f77d1e0e5
> - libMesh from Git commit 19706028f
> - a bunch of packagees from repositories (cgns 3.4.0-2, hdf5-openmpi 
> 1.10.5-1, hdf5-openmpi 1.10.5-1, netcdf-openmpi 4.7.1-2, paraview 5.7.0-3, 
> pnetcdf-openmpi 1.12.0-1, python-h5py-openmpi 2.10.0-1, vtk 8.2.0-9, hwloc 
> 2.1.0-2, metis 5.1.0.p7-1, openmp 9.0.0-2, openmpi 4.0.2-3, suitesparse 
> 5.6.0-1, scotch 6.0.6-1)
> - some from AUR's user-contributed packages (fftw-mpi 3.3.8-1, hypre-sm 
> 2.14.0-1, mumps 5.2.1-3, superlu 5.2.1-9)
>
> If you want to try, my recipe is here:
> https://notabug.org/broncodev/libmesh-pkgbuild.git (commit e3d46fc)

I was going to say that there's no way for us to link against an
external netcdf without actually changing our netcdf.m4 file, then I
followed this link to find a patch against our netcdf.m4 file.  So
you're at least on the right track!

I don't have time to check this out myself right now but I'll throw up
a PR with it so we don't lose track of it and so we can see what our
CI thinks of it.  Thanks!

> https://notabug.org/broncodev/petsc-pkgbuild.git (commit 3e9d679)
>
> MUMPS is still not detected by libMesh :( .

Is configure finding your petscconf.h?  Is PETSC_HAVE_MUMPS defined
there?
---
Roy

Re: [Libmesh-users] how to compile with installed netcdf?

From: <ed...@op...> - 2019-12-30 21:43:21

On 2019-12-30 17:26, Stogner, Roy H wrote:
> ----8< snip ----
>> MUMPS is still not detected by libMesh :( .
> 
> Is configure finding your petscconf.h?  Is PETSC_HAVE_MUMPS defined
> there?

I looked into =configure=, and found this:

     $as_echo "#define PETSC_HAVE_MUMPS 1" >>confdefs.h

Then found this in config.status:

     D["PETSC_HAVE_MUMPS"]=" 1"

Then, my config.log shows:

    ----8< snip ----
     configure:6861: mpicxx -c -fPIC -fopenmp -march=amdfam10 
-mtune=generic -fPIC -fopenmp -march=amdfam10 -mtune=generic -O2 
-D_FORTIFY_SOURCE=2 conftest.cpp >&5
     conftest.cpp: In function 'int main()':
     conftest.cpp:18:9: error: 'thisisanerror' was not declared in this 
scope
        18 |         thisisanerror;
           |         ^~~~~~~~~~~~~
     configure:6861: $? = 1
     configure: failed program was:
     | /* confdefs.h */
     ----8< snip ----
     | #define PETSC_HAVE_MUMPS 1
     ----8< snip ----

but I cannot find conftest.cpp. This put a question mark on my face :) .

P.S. If you don't get direct e-mails from me, it's because I can't 
(https://ut.service-now.com/sp?id=kb_article&number=KB0011416)

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Re: [Libmesh-users] how to compile with installed netcdf?

From: Stogner, R. H <roy...@ic...> - 2019-12-30 17:34:03

On Mon, 30 Dec 2019, ed...@op... wrote:

> I think that I found a way to use my system's netcdf with libMesh (make check 
> gave no errors).

> If you want to try, my recipe is here:
> https://notabug.org/broncodev/libmesh-pkgbuild.git (commit e3d46fc)

This (plus a bootstrap commit) is now also a PR at
https://github.com/libMesh/libmesh/pull/2388 - thanks again.
---
Roy

Re: [Libmesh-users] how to compile with installed netcdf?

From: <ed...@op...> - 2019-12-30 21:20:37

Attachments: configure_libmesh_netcdf_no_parmetis.out

On 2019-12-30 17:33, Stogner, Roy H wrote:
> ----8<---- snip
> This (plus a bootstrap commit) is now also a PR at
> https://github.com/libMesh/libmesh/pull/2388 - thanks again.

Thanks to you for libMesh. I saw the comments on the PR, and I want to 
share the output of my =configure= (attached). In summary:

    exodus........................... : yes

If you need more information, let me know, although you can see how I 
compile with the repos https://notabug.org/broncodev. In particular, 
remember that I forced the library with =netcdf.m4= (look for this

   #+begin_src autoconf
     LIBS="$LIBS -lnetcdf -L/usr/lib"
     CPPFLAGS="$CPPFLAGS -I/usr/include"
   #+end_src

which may be different in your system), and this in my PKGBUILD (the 
recipe to compile):

   #+begin_SRC bash
     [[ -f /usr/include/netcdf.h ]] && \
         sed -i "s-\(ac_subdirs_all='\)contrib/netcdf/v4-\1-g; 
s-\(subdirs=\"\$subdirs\) contrib/netcdf/v4-\1-g" configure
   #+end_SRC

Happy new year!

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