Re: [Fink-beginners] Openmpi fails to build

[Alexander Hansen]

> On Nov 18, 2016, at 21:08, Marc Boxerman  wrote:
> 
> I cannot update openmpi.  Here’s the output immediately before and at the 
> error:
> 
> -I/sw/include
> /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 
> -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT 
> adio/ad_nfs/ad_nfs_features.lo -MD -MP -MF 
> adio/ad_nfs/.deps/ad_nfs_features.Tpo -c adio/ad_nfs/ad_nfs_features.c 
> -fno-common -DPIC -o adio/ad_nfs/.libs/ad_nfs_features.o -I. -I./adio/include 
> -I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
> -I./mpi-io -I./adio/include -I./include 
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include
>  -I/sw/include
> libtool:   error: Failed to create 'mpi-io/.libs'
> make[4]: *** [Makefile:3396: mpi-io/get_posn.lo] Error 1
> libtool:   error: Failed to create 'mpi-io/.libs'
> make[4]: *** [Makefile:3396: mpi-io/get_size.lo] Error 1
> libtool:   error: Failed to create 'mpi-io/.libs'
> make[4]: *** [Makefile:3396: mpi-io/iread.lo] Error 1
> make[4]: Leaving directory 
> '/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio'
> make[3]: *** [all-recursive] Error 1
> make[2]: *** [all-recursive] Error 1
> make[1]: *** [all-recursive] Error 1
> make: *** [all-recursive] Error 1
> ### execution of /tmp/fink.zJauj failed, exit code 2
> ### execution of /tmp/fink.x0WgO failed, exit code 2
> Removing runtime build-lock...
> Removing build-lock package...
> /sw/bin/dpkg-lockwait -r fink-buildlock-openmpi-1.10.4-1
> (Reading database ... 265512 files and directories currently installed.)
> Removing fink-buildlock-openmpi-1.10.4-1 ...
> Failed: phase compiling: openmpi-1.10.4-1 failed
> 
> I’m still running El Capitan.
> 
> Thank you for any assistance,
> 
> Marc
> 

How many build jobs is fink set up for?  If it’s more than one could you make 
an another attempt with only one job?  The output kind of looks like there 
might have been an earlier failure in another build thread.

-- 
Alexander Hansen, Ph.D.
Fink User Liaison


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Re: [Fink-beginners] Openmpi fails to build

[Alexander Hansen]

> On Nov 20, 2016, at 16:46, Marc Boxerman  wrote:
> 
> You’re right.  Fink updated openmpi and openmpi-shlibs together.  Fink will 
> not let me update openmpi without also updating openmpi-shlibs.  I tried 
> updating only openmpi-shlibs.  It also fails  The output suggests fink was 
> also attempting to update openmpi?

There is no possible way in the current packaging to build one without the 
other because they’re built as part of the same procedure.  

In principle we could build them separately, but there’s really not a 
circumstance where there is a gain from building the headers and other 
build-time items in  a separate operation for the same version of a package.

> 
> -1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent 
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include
>  -I/sw/include
> /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 
> -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT 
> adio/ad_testfs/ad_testfs_open.lo -MD -MP -MF 
> adio/ad_testfs/.deps/ad_testfs_open.Tpo -c adio/ad_testfs/ad_testfs_open.c 
> -fno-common -DPIC -o adio/ad_testfs/.libs/ad_testfs_open.o -I. 
> -I./adio/include -I./../../../../../opal/include 
> -I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include 
> -I./include 
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
>  -I/sw/src/fink.build/openmpi-1.10.4-1/open/sw/bin/flag-sort: /usr/bin/clang 
> -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing 
> -DHAVE_ROMIOCONF_H -MT adio/ad_ufs/ad_ufs_open.lo -MD -MP -MF 
> adio/ad_ufs/.deps/ad_ufs_open.Tpo -c adio/ad_ufs/ad_ufs_open.c -fno-common 
> -DPIC -o adio/ad_ufs/.libs/ad_ufs_open.o -I. -I./adio/include 
> -I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
> -I./mpi-io -I./adio/include -I./include 
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/r4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include
>  -I/sw/include
> /sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 
> -DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_fcntl.lo 
> -MD -MP -MF adio/common/.deps/ad_fcntl.Tpo -c adio/common/ad_fcntl.c 
> -fno-common -DPIC -o adio/common/.libs/ad_fcntl.o -I. -I./adio/include 
> -I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
> -I./mpi-io -I./adio/include -I./include 
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
>  
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/a/sw/bin/flag-sort:
>  /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG 
> -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_end.lo -MD -MP -MF 
> adio/common/.deps/ad_end.Tpo -c adio/common/ad_end.c -fno-common -DPIC -o 
> adio/common/.libs/ad_end.o -I. -I./adio/include 
> -I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
> -I./mpi-io -I./adio/include -I./include 
> -I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
>  
> 

Re: [Fink-beginners] Openmpi fails to build

[Marc Boxerman]

You’re right.  Fink updated openmpi and openmpi-shlibs together.  Fink will not 
let me update openmpi without also updating openmpi-shlibs.  I tried updating 
only openmpi-shlibs.  It also fails  The output suggests fink was also 
attempting to update openmpi?

-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include
 -I/sw/include
/sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 
-DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT 
adio/ad_testfs/ad_testfs_open.lo -MD -MP -MF 
adio/ad_testfs/.deps/ad_testfs_open.Tpo -c adio/ad_testfs/ad_testfs_open.c 
-fno-common -DPIC -o adio/ad_testfs/.libs/ad_testfs_open.o -I. -I./adio/include 
-I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
-I./mpi-io -I./adio/include -I./include 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
 -I/sw/src/fink.build/openmpi-1.10.4-1/open/sw/bin/flag-sort: /usr/bin/clang 
-DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG -fno-strict-aliasing 
-DHAVE_ROMIOCONF_H -MT adio/ad_ufs/ad_ufs_open.lo -MD -MP -MF 
adio/ad_ufs/.deps/ad_ufs_open.Tpo -c adio/ad_ufs/ad_ufs_open.c -fno-common 
-DPIC -o adio/ad_ufs/.libs/ad_ufs_open.o -I. -I./adio/include 
-I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
-I./mpi-io -I./adio/include -I./include 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/r4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/opal/mca/event/libevent2021/libevent/include
 -I/sw/include
/sw/bin/flag-sort: /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 
-DNDEBUG -fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_fcntl.lo 
-MD -MP -MF adio/common/.deps/ad_fcntl.Tpo -c adio/common/ad_fcntl.c 
-fno-common -DPIC -o adio/common/.libs/ad_fcntl.o -I. -I./adio/include 
-I./../../../../../opal/include -I./../../../../../ompi/include -I./include 
-I./mpi-io -I./adio/include -I./include 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/a/sw/bin/flag-sort:
 /usr/bin/clang -DHAVE_CONFIG_H -DOMPI_BUILDING=1 -O3 -DNDEBUG 
-fno-strict-aliasing -DHAVE_ROMIOCONF_H -MT adio/common/ad_end.lo -MD -MP -MF 
adio/common/.deps/ad_end.Tpo -c adio/common/ad_end.c -fno-common -DPIC -o 
adio/common/.libs/ad_end.o -I. -I./adio/include -I./../../../../../opal/include 
-I./../../../../../ompi/include -I./include -I./mpi-io -I./adio/include 
-I./include 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../..
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/../../../../../opal/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/include
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/mpi-io
 
-I/sw/src/fink.build/openmpi-1.10.4-1/openmpi-1.10.4/ompi/mca/io/romio/romio/adio/inclmpi-1.10.4/ompi/mca/io/romio/romio/adio/include