Hello Tomek,

I’m sorry to hear that you are having problems building APBS, and hopefully we’ll be able to get it sorted out quickly.  First off, would you mind trying to compile the latest source?  Or is there a specific reason that you are using 1.3?

Could you also let me know what operating system, and which version you are using?  Finally, sending me a copy of your build output will be helpful in getting you up and running.

Best regards,

 - Keith


From: Tomek Wlodarski <tomek.wlodarski@gmail.com>
Date: Monday, February 10, 2014 at 9:37 AM
To: "apbs-users@googlegroups.com" <apbs-users@googlegroups.com>
Cc: David Hall <lists@cowsandmilk.net>, "Jurrus, Elizabeth R" <Elizabeth.Jurrus@pnnl.gov>, Keith Fligg <keith@pnnl.gov>, "apbs-users@lists.sourceforge.net" <apbs-users@lists.sourceforge.net>, "Baker, Nathan" <Nathan.Baker@pnnl.gov>
Subject: Re: [apbs-users] compiling APBS 1.4.1 with MPI support

Hi,

I am completely new to apbs and I came across same error with MPI.
I was wondering if there is anything new regarding to MPI support in apbs1.4.x ?

if not then how can I compile apbs-1.3 with MPI support?
Which flag or option I have to use?
Thank you,
Best!

tomek

W dniu czwartek, 30 stycznia 2014 14:11:06 UTC u¿ytkownik Baker, Nathan napisa³:

OK, thank you for the clarification.

 

Keith, we should probably update package names and make sure the next release is consistent.

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: David Hall [mailto:li...@cowsandmilk.net]
Sent: Thursday, January 30, 2014 6:10 AM
To: apbs-...@googlegroups.com
Cc: apbs-...@lists.sourceforge.net; Baker, Nathan
Subject: Re: [apbs-users] compiling APBS 1.4.1 with MPI support

 

I feel the need to point out here that if you download the source to apbs from sourceforge, the source in APBS-1.4-source.tar.gz will produce binaries that say Version 1.4.1 when you run apbs --version. The CMakeLists.txt has a line that says set(APBS_VERSION "1.4.1")

That is good reason for people doing a build from source to believe they are working with 1.4.1

-David

On Tuesday, January 14, 2014 11:21:47 PM UTC-5, Baker, Nathan wrote:

Hi Kevin –

 

I think someone mistook the Ubuntu-bundled package 1.4-1 for “1.4.1”.  1.4.0 is the latest release of APBS.

 

Thanks,

 

--

Nathan Baker

Laboratory Fellow and Technical Group Manager

Applied Statistics and Computational Modeling

Pacific Northwest National Laboratory

+1-509-375-3997

http://www.linkedin.com/in/nathanandrewbaker/

 

From: Kevin Abbey [mailto:kevinabbe...@gmail.com]
Sent: Monday, January 13, 2014 9:23 AM
To: apbs-...@googlegroups.com
Cc: apbs-...@lists.sourceforge.net
Subject: Re: [apbs-users] compiling APBS 1.4.1 with MPI support

 

Hi,

I found the same problem but with 1.4.  I don't see 1.4.1 listed.

Is there any update on this?

 

Kevin



On Thursday, November 29, 2012 8:17:30 AM UTC-5, Miguel Ortiz Lombardía wrote:

Hi,

Perhaps this has been discussed earlier in the list, but I couldn't find
any relevant information. If so, please excuse me and send me a link
with that information.

I would like to compile APBS 1.4.1 with MPI support. Following the
documentation on the compilation via cmake does not seem to generate an
MPI-compatible binary, even if I can see that MPI libraries are found
and that I get a "MPI enabled" message.

On running apbs (mpirun -n <n> apbs ...) I always get:

> NOsh_setupCalcMGPARA:  Oops!  You're trying to perform an 'mg-para' (parallel) calculation
> NOsh_setupCalcMGPARA:  with a version of APBS that wasn't compiled with MPI!

I have tried to compile with:

CC=mpicc CXX=mpicxx cmake ..
CC=mpicc CXX=mpicxx make

to force the use of the mpi compilers (based on intel compilers
12.1.0.20120928) but the produced binary gives the same runtime error.

I forgot to say, this is on a mac with Snow Leopard Server (10.6.8)

Cheers,

--
Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.orti...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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