On 2013-02-18, at 2:45 PM, Jack Howarth wrote:
> On Mon, Feb 18, 2013 at 06:30:10PM +0000, Dmitry Rodionov wrote:
>> [ 64%] Building C object src/mdlib/CMakeFiles/md.dir/wnblist.c.o
>> Linking C shared library libmd_mpi.dylib
>> [ 64%] Built target md
>> make: *** [all] Error 2
>> ### execution of /tmp/fink.6dfnm failed, exit code 2
>> ### execution of /tmp/fink.U_Vpg failed, exit code 2
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-gromacs-mpi-openmpi-4.6-1
>> (Reading database ... 279256 files and directories currently installed.)
>> Removing fink-buildlock-gromacs-mpi-openmpi-4.6-1 ...
>> Failed: phase compiling: gromacs-mpi-openmpi-4.6-1 failed
>>
>>
>> Package manager version: 0.34.5
>> Distribution version: selfupdate-rsync Mon Feb 18 13:06:45 2013, 10.6, x86_64
>> Trees: local/main stable/main unstable/main unstable/crypto
>> Xcode.app: 3.2.6
>> Xcode command-line tools: 3.2.6
>> Max. Fink build jobs: 4
>>
>> Interestingly, with jobs=1 it fails earlier:
>>
>> [ 53%] Building C object share/template/CMakeFiles/template.dir/template.c.o
>> In file included from /sw/include/gromacs/futil.h:45:0,
>> from /sw/include/gromacs/filenm.h:49,
>> from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:32:
>> /sw/include/gromacs/typedefs.h:92:31: error: unknown type name 'bool'
>> /sw/include/gromacs/typedefs.h:129:33: error: unknown type name 'bool'
>> /sw/include/gromacs/typedefs.h:140:48: error: unknown type name 'bool'
>> /sw/include/gromacs/typedefs.h:153:47: error: unknown type name 'bool'
>> /sw/include/gromacs/typedefs.h:157:34: error: unknown type name 'bool'
>> In file included from /sw/include/gromacs/filenm.h:49:0,
>> from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:32:
>> /sw/include/gromacs/futil.h:67:1: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:70:1: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:73:1: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:82:1: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:99:1: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:109:1: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:111:47: error: unknown type name 'bool'
>> /sw/include/gromacs/futil.h:113:43: error: unknown type name 'bool'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:32:0:
>> /sw/include/gromacs/filenm.h:82:8: error: unknown type name 'bool'
>> /sw/include/gromacs/filenm.h:113:1: error: unknown type name 'bool'
>> /sw/include/gromacs/filenm.h:116:1: error: unknown type name 'bool'
>> /sw/include/gromacs/filenm.h:130:1: error: unknown type name 'bool'
>> /sw/include/gromacs/filenm.h:133:1: error: unknown type name 'bool'
>> /sw/include/gromacs/filenm.h:136:1: error: unknown type name 'bool'
>> In file included from /sw/include/gromacs/statutil.h:51:0,
>> from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:36:
>> /sw/include/gromacs/readinp.h:48:3: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:49:3: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:57:6: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:69:21: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:103:3: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:111:5: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:118:9: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:125:1: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:135:1: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:143:1: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:145:59: error: unknown type name 'bool'
>> /sw/include/gromacs/readinp.h:147:43: error: unknown type name 'bool'
>> In file included from /sw/include/gromacs/statutil.h:52:0,
>> from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:36:
>> /sw/include/gromacs/wman.h:57:9: error: unknown type name 'bool'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:36:0:
>> /sw/include/gromacs/statutil.h:60:3: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:70:1: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:93:43: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:132:1: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:132:51: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:143:57: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:210:1: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:223:1: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:242:1: error: unknown type name 'bool'
>> /sw/include/gromacs/statutil.h:245:1: error: unknown type name 'bool'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:37:0:
>> /sw/include/gromacs/xvgr.h:83:1: error: unknown type name 'bool'
>> /sw/include/gromacs/xvgr.h:150:8: error: unknown type name 'bool'
>> /sw/include/gromacs/xvgr.h:151:8: error: unknown type name 'bool'
>> /sw/include/gromacs/xvgr.h:152:8: error: unknown type name 'bool'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:38:0:
>> /sw/include/gromacs/gmx_fatal.h:149:16: error: unknown type name 'bool'
>> /sw/include/gromacs/gmx_fatal.h:175:1: error: unknown type name 'bool'
>> /sw/include/gromacs/gmx_fatal.h:179:1: error: unknown type name 'bool'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/build/share/template/gromacs/trajana.h:70:0,
>> from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:41:
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/build/share/template/gromacs/selection.h:164:20:
>> error: unknown type name 'output_env_t'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:41:0:
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/build/share/template/gromacs/trajana.h:223:19:
>> error: unknown type name 'output_env_t'
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:
>> In function 'gmx_template':
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:145:5:
>> error: unknown type name 'output_env_t'
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:160:5:
>> warning: implicit declaration of function 'parse_trjana_args'
>> [-Wimplicit-function-declaration]
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:192:25:
>> error: too many arguments to function 'xvgropen'
>> In file included from
>> /sw/src/fink.build/gromacs-mpi-openmpi-4.6-1/gromacs-4.6/share/template/template.c:37:0:
>> /sw/include/gromacs/xvgr.h:86:14: note: declared here
>> make[2]: *** [share/template/CMakeFiles/template.dir/template.c.o] Error 1
>> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
>> make: *** [all] Error 2
>> ### execution of /tmp/fink.J_9_t failed, exit code 2
>> ### execution of /tmp/fink.084nQ failed, exit code 2
>> Removing runtime build-lock...
>> Removing build-lock package...
>> /sw/bin/dpkg-lockwait -r fink-buildlock-gromacs-mpi-openmpi-4.6-1
>> (Reading database ... 279256 files and directories currently installed.)
>> Removing fink-buildlock-gromacs-mpi-openmpi-4.6-1 ...
>> Failed: phase compiling: gromacs-mpi-openmpi-4.6-1 failed
>>
>> Same error happens with jobs=4, but somehow the process continues.
>
>
> What do you get for...
>
> dpkg -S /sw/include/gromacs/xvgr.h
>
> I would have expected gromacs-dev if your previously installed gromacs is
> 4.5.6. Also what do you have from the output of...
>
> dpkg -l | grep gromacs
>
> The current packaging BuildConflicts gromacs-dev but if you have some really
> old version of gromacs installed before the headers got moved into gromacs-dev
> that could be the problem.
>
% dpkg -S /sw/include/gromacs/xvgr.h
gromacs-mpi-openmpi: /sw/include/gromacs/xvgr.h
and
% dpkg -l | grep gromacs
ii gromacs-mpi-op 4.0.5-1004 Molecular dynamics package (Parallel version
ii gromacs-mpi-op 4.0.5-1004 Molecular dynamics package (Parallel version
I removed the old gromacs and the building process went fine.
Thanks!
Regards,
Dmitry
------------------------------------------------------------------------------
The Go Parallel Website, sponsored by Intel - in partnership with Geeknet,
is your hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials, tech docs,
whitepapers, evaluation guides, and opinion stories. Check out the most
recent posts - join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Fink-users mailing list
Fink-users@lists.sourceforge.net
List archive:
http://news.gmane.org/gmane.os.macosx.fink.user
Subscription management:
https://lists.sourceforge.net/lists/listinfo/fink-users
