Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Jeff Hammond]

You must be using an older version of Gromacs, because the version I'm
looking at (git master) has nary a reference to the C++ bindings.

Since you say that Gromacs alone compiles fine, I suspect the problem
is that Plumed uses the C++ bindings.  The Plumed download site hosted
by Google Docs (yuck!) is down/broken/in-redirect-hell so I can't
verify this hypothesis right now.

Jeff

On Tue, Jul 9, 2013 at 8:44 AM, Jeff Squyres (jsquyres)
 wrote:
> If you care, the issue is that it looks like Gromacs is using the MPI C++ 
> bindings.  You therefore need to use the MPI C++ wrapper compiler, mpic++ 
> (vs. mpicc, which is the MPI C wrapper compiler).
>
>
> On Jul 9, 2013, at 9:41 AM, Tomek Wlodarski  wrote:
>
>> I used mpicc but when I switched in Makefile to mpic++ it compiled
>> without errors.
>> Thanks a lot!
>> Best,
>>
>> tomek
>>
>> On Tue, Jul 9, 2013 at 2:31 PM, Jeff Squyres (jsquyres)
>>  wrote:
>>> I don't see all the info requested from that web page, but it looks like 
>>> OMPI built the C++ bindings ok.
>>>
>>> Did you use mpic++ to build Gromacs?
>>>
>>>
>>> On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski  
>>> wrote:
>>>
 So I am running OpenMPi1.6.3 (config.log attached)
 And I would like to install gromacs patched with plumed (scientific
 computing). Both uses openmpi.
 Gromacs alone compiles without errors (openMPI works). But when
 patched I got one mentioned before.
 I am sending config file for patched gromacs.
 If you need any other file I would be happy to provide.
 Thanks a lot!
 Best,

 tomek
 ___
 users mailing list
 us...@open-mpi.org
 http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>>
>>> --
>>> Jeff Squyres
>>> jsquy...@cisco.com
>>> For corporate legal information go to: 
>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>
>>>
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to: 
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users



-- 
Jeff Hammond
jeff.scie...@gmail.com

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Tomek Wlodarski]

Oh you are right.
Thanks.
Best

tomek

On Tue, Jul 9, 2013 at 2:44 PM, Jeff Squyres (jsquyres)
 wrote:
> If you care, the issue is that it looks like Gromacs is using the MPI C++ 
> bindings.  You therefore need to use the MPI C++ wrapper compiler, mpic++ 
> (vs. mpicc, which is the MPI C wrapper compiler).
>
>
> On Jul 9, 2013, at 9:41 AM, Tomek Wlodarski  wrote:
>
>> I used mpicc but when I switched in Makefile to mpic++ it compiled
>> without errors.
>> Thanks a lot!
>> Best,
>>
>> tomek
>>
>> On Tue, Jul 9, 2013 at 2:31 PM, Jeff Squyres (jsquyres)
>>  wrote:
>>> I don't see all the info requested from that web page, but it looks like 
>>> OMPI built the C++ bindings ok.
>>>
>>> Did you use mpic++ to build Gromacs?
>>>
>>>
>>> On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski  
>>> wrote:
>>>
 So I am running OpenMPi1.6.3 (config.log attached)
 And I would like to install gromacs patched with plumed (scientific
 computing). Both uses openmpi.
 Gromacs alone compiles without errors (openMPI works). But when
 patched I got one mentioned before.
 I am sending config file for patched gromacs.
 If you need any other file I would be happy to provide.
 Thanks a lot!
 Best,

 tomek
 ___
 users mailing list
 us...@open-mpi.org
 http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>>
>>> --
>>> Jeff Squyres
>>> jsquy...@cisco.com
>>> For corporate legal information go to: 
>>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>>
>>>
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to: 
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Jeff Squyres (jsquyres)]

If you care, the issue is that it looks like Gromacs is using the MPI C++ 
bindings.  You therefore need to use the MPI C++ wrapper compiler, mpic++ (vs. 
mpicc, which is the MPI C wrapper compiler).


On Jul 9, 2013, at 9:41 AM, Tomek Wlodarski  wrote:

> I used mpicc but when I switched in Makefile to mpic++ it compiled
> without errors.
> Thanks a lot!
> Best,
> 
> tomek
> 
> On Tue, Jul 9, 2013 at 2:31 PM, Jeff Squyres (jsquyres)
>  wrote:
>> I don't see all the info requested from that web page, but it looks like 
>> OMPI built the C++ bindings ok.
>> 
>> Did you use mpic++ to build Gromacs?
>> 
>> 
>> On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski  
>> wrote:
>> 
>>> So I am running OpenMPi1.6.3 (config.log attached)
>>> And I would like to install gromacs patched with plumed (scientific
>>> computing). Both uses openmpi.
>>> Gromacs alone compiles without errors (openMPI works). But when
>>> patched I got one mentioned before.
>>> I am sending config file for patched gromacs.
>>> If you need any other file I would be happy to provide.
>>> Thanks a lot!
>>> Best,
>>> 
>>> tomek
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> 
>> 
>> --
>> Jeff Squyres
>> jsquy...@cisco.com
>> For corporate legal information go to: 
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>> 
>> 
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users


-- 
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to: 
http://www.cisco.com/web/about/doing_business/legal/cri/

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Tomek Wlodarski]

I used mpicc but when I switched in Makefile to mpic++ it compiled
without errors.
Thanks a lot!
Best,

tomek

On Tue, Jul 9, 2013 at 2:31 PM, Jeff Squyres (jsquyres)
 wrote:
> I don't see all the info requested from that web page, but it looks like OMPI 
> built the C++ bindings ok.
>
> Did you use mpic++ to build Gromacs?
>
>
> On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski  wrote:
>
>> So I am running OpenMPi1.6.3 (config.log attached)
>> And I would like to install gromacs patched with plumed (scientific
>> computing). Both uses openmpi.
>> Gromacs alone compiles without errors (openMPI works). But when
>> patched I got one mentioned before.
>> I am sending config file for patched gromacs.
>> If you need any other file I would be happy to provide.
>> Thanks a lot!
>> Best,
>>
>> tomek
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to: 
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Jeff Squyres (jsquyres)]

I don't see all the info requested from that web page, but it looks like OMPI 
built the C++ bindings ok.

Did you use mpic++ to build Gromacs?


On Jul 9, 2013, at 9:20 AM, Tomek Wlodarski  wrote:

> So I am running OpenMPi1.6.3 (config.log attached)
> And I would like to install gromacs patched with plumed (scientific
> computing). Both uses openmpi.
> Gromacs alone compiles without errors (openMPI works). But when
> patched I got one mentioned before.
> I am sending config file for patched gromacs.
> If you need any other file I would be happy to provide.
> Thanks a lot!
> Best,
> 
> tomek
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users


-- 
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to: 
http://www.cisco.com/web/about/doing_business/legal/cri/

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Tomek Wlodarski]

So I am running OpenMPi1.6.3 (config.log attached)
And I would like to install gromacs patched with plumed (scientific
computing). Both uses openmpi.
Gromacs alone compiles without errors (openMPI works). But when
patched I got one mentioned before.
I am sending config file for patched gromacs.
If you need any other file I would be happy to provide.
Thanks a lot!
Best,

tomek


config_gromacs.log.bz2
Description: BZip2 compressed data


config_openmpi.log.bz2
Description: BZip2 compressed data

Re: [OMPI users] undefined reference to `MPI::Comm::Comm()

[Jeff Squyres (jsquyres)]

Please send all the information listed here:

http://www.open-mpi.org/community/help/


On Jul 9, 2013, at 8:36 AM, Tomek Wlodarski  wrote:

> Hi,
> 
> I am trying to locally compile software which uses openmpi (1.6.3),
> but I got this error:
> 
> restraint_camshift2.o:(.toc+0x98): undefined reference to
> `ompi_mpi_cxx_op_intercept'
> restraint_camshift2.o: In function `Intracomm':
> /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25:
> undefined reference to `MPI::Comm::Comm()'
> /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25:
> undefined reference to `MPI::Comm::Comm()'
> restraint_camshift2.o: In function `Intracomm':
> /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm_inln.h:23:
> undefined reference to `MPI::Comm::Comm()'
> restraint_camshift2.o: In function `Intracomm':
> /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25:
> undefined reference to `MPI::Comm::Comm()'
> /home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25:
> undefined reference to `MPI::Comm::Comm()'
> restraint_camshift2.o:/home/users/didymos/openmpi-1.6.3/include/openmpi/ompi/mpi/cxx/intracomm.h:25:
> more undefined references to `MPI::Comm::Comm()' follow
> restraint_camshift2.o:(.data.rel.ro._ZTVN3MPI3WinE[_ZTVN3MPI3WinE]+0x48):
> undefined reference to `MPI::Win::Free()'
> restraint_camshift2.o:(.data.rel.ro._ZTVN3MPI8DatatypeE[_ZTVN3MPI8DatatypeE]+0x78):
> undefined reference to `MPI::Datatype::Free()'
> collect2: error: ld returned 1 exit status
> make[3]: *** [mdrun] Error 1
> make[3]: Leaving directory `/home/users/didymos/src/gromacs-4.5.5/src/kernel'
> make[2]: *** [all-recursive] Error 1
> make[2]: Leaving directory `/home/users/didymos/src/gromacs-4.5.5/src'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/home/users/didymos/src/gromacs-4.5.5/src'
> make: *** [all-recursive] Error 1
> 
> I am using gcc 4.7.3
> Any ideas or suggestions?
> Thanks!
> Best,
> 
> tomek
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users


-- 
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to: 
http://www.cisco.com/web/about/doing_business/legal/cri/