Re: [Fink-beginners] Openmpi fails to build

[Marc Boxerman]

That indeed was the case.  All is well now.

Thanks for all your help.

Marc

> On Nov 22, 2016, at 11:52 AM, Alexander Hansen  
> wrote:
> 
> 
>> On Nov 22, 2016, at 09:50, Marc Boxerman  wrote:
>> 
>> Thanks, Alexander.
>> 
>> I logged off all other users and quit all applications except Finder and 
>> Terminal.  
>> Openmpi appears to have built successfully.  
>> But oddly, fink list -o still lists openmpi and openmpi-shlibs as 
>> uninstalled at the version numbers I just built.
>> 
>> Here’s how the build ended.  It looks normal to me.
>> 
>> Reverting ownership of install dir to root
>> Writing control file...
>> Writing package script postinst...
>> Writing package script prerm...
>> Writing md5sums file...
>> env LANG=C LC_ALL=C dpkg-deb -b root-openmpi-1.10.4-1 
>> /sw/fink/10.11/stable/main/binary-darwin-x86_64/devel
>> dpkg-deb: building package `openmpi' in 
>> `/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.4-1_darwin-x86_64.deb'.
>> Reverting ownership of install dir to root
>> Writing control file...
>> Creating shlibs files...
>> Writing md5sums file...
>> env LANG=C LC_ALL=C dpkg-deb -b root-openmpi-shlibs-1.10.4-1 
>> /sw/fink/10.11/stable/main/binary-darwin-x86_64/devel
>> dpkg-deb: building package `openmpi-shlibs' in 
>> `/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.10.4-1_darwin-x86_64.deb'.
>> 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 ...
>> Updating the list of locally available binary packages.
>> Scanning dists/stable/main/binary-darwin-x86_64
>> New package: 
>> dists/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.10.4-1_darwin-x86_64.deb
>> New package: 
>> dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.4-1_darwin-x86_64.deb
>> 
>> Marc
> 
> It looks like they got built but not installed.  Try “fink install openmpi”.
> 
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> 


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Re: [Fink-beginners] Openmpi fails to build

[Alexander Hansen]

> On Nov 22, 2016, at 09:50, Marc Boxerman  wrote:
> 
> Thanks, Alexander.
> 
> I logged off all other users and quit all applications except Finder and 
> Terminal.  
> Openmpi appears to have built successfully.  
> But oddly, fink list -o still lists openmpi and openmpi-shlibs as uninstalled 
> at the version numbers I just built.
> 
> Here’s how the build ended.  It looks normal to me.
> 
> Reverting ownership of install dir to root
> Writing control file...
> Writing package script postinst...
> Writing package script prerm...
> Writing md5sums file...
> env LANG=C LC_ALL=C dpkg-deb -b root-openmpi-1.10.4-1 
> /sw/fink/10.11/stable/main/binary-darwin-x86_64/devel
> dpkg-deb: building package `openmpi' in 
> `/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.4-1_darwin-x86_64.deb'.
> Reverting ownership of install dir to root
> Writing control file...
> Creating shlibs files...
> Writing md5sums file...
> env LANG=C LC_ALL=C dpkg-deb -b root-openmpi-shlibs-1.10.4-1 
> /sw/fink/10.11/stable/main/binary-darwin-x86_64/devel
> dpkg-deb: building package `openmpi-shlibs' in 
> `/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.10.4-1_darwin-x86_64.deb'.
> 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 ...
> Updating the list of locally available binary packages.
> Scanning dists/stable/main/binary-darwin-x86_64
> New package: 
> dists/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.10.4-1_darwin-x86_64.deb
> New package: 
> dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.4-1_darwin-x86_64.deb
> 
> Marc

It looks like they got built but not installed.  Try “fink install openmpi”.

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


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Re: [Fink-beginners] Openmpi fails to build

[Marc Boxerman]

Thanks, Alexander.

I logged off all other users and quit all applications except Finder and 
Terminal.  
Openmpi appears to have built successfully.  
But oddly, fink list -o still lists openmpi and openmpi-shlibs as uninstalled 
at the version numbers I just built.

Here’s how the build ended.  It looks normal to me.

Reverting ownership of install dir to root
Writing control file...
Writing package script postinst...
Writing package script prerm...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-openmpi-1.10.4-1 
/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel
dpkg-deb: building package `openmpi' in 
`/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.4-1_darwin-x86_64.deb'.
Reverting ownership of install dir to root
Writing control file...
Creating shlibs files...
Writing md5sums file...
env LANG=C LC_ALL=C dpkg-deb -b root-openmpi-shlibs-1.10.4-1 
/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel
dpkg-deb: building package `openmpi-shlibs' in 
`/sw/fink/10.11/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.10.4-1_darwin-x86_64.deb'.
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 ...
Updating the list of locally available binary packages.
Scanning dists/stable/main/binary-darwin-x86_64
New package: 
dists/stable/main/binary-darwin-x86_64/devel/openmpi-shlibs_1.10.4-1_darwin-x86_64.deb
New package: 
dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.4-1_darwin-x86_64.deb

Marc

> On Nov 22, 2016, at 10:59 AM, Alexander Hansen  
> wrote:
> 
> 
>> On Nov 22, 2016, at 08:31, Alexander Hansen  
>> wrote:
>> 
>> 
>>> On Nov 21, 2016, at 22:37, Marc Boxerman  wrote:
>>> 
>>> Alexander,
>>> 
>>> The build still failed using fink -l build openmpi.  I’m not sure what you 
>>> mean by the output getting “swallowed” but the build output went to stdout 
>>> as well as to the log file.  I’m attaching the log file for your review. 
>>> 
>>> Thanks for your continued assistance.
>>> 
>>> Marc
>>> 
>> 
>> By “swallowed”  I mean: “overwritten and lost”, e.g. due to something trying 
>> to be cute with control characters.
>> 
>> I’ll generate a log file here and do a diff.
>> 
>> -- 
>> Alexander Hansen, Ph.D.
>> Fink User Liaison
>> 
> 
> I had a log file from yesterday’s test.  I found the issue, I think.  There 
> was indeed an earlier error:
> 
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_fstype.lo] Error 128
> make[4]: *** Waiting for unfinished jobs
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_iread_fake.lo] Error 128
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_opencoll_scalable.lo] Error 128
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_subarray.lo] Error 129
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_write_nolock.lo] Error 128
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_write_coll.lo] Error 128
> make[4]: *** [Makefile:3396: adio/common/ad_write_str_naive.lo] Error 129
> ./libtool: fork: Resource temporarily unavailable
> make[4]: *** [Makefile:3396: adio/common/ad_iwrite_fake.lo] Error 129
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> ./libtool: fork: Resource temporarily unavailable
> 
> :   error: Failed to create 'adio/common/.libs'
> make[4]: *** 

Re: [Fink-beginners] Openmpi fails to build

[Alexander Hansen]

> On Nov 22, 2016, at 08:31, Alexander Hansen  
> wrote:
> 
> 
>> On Nov 21, 2016, at 22:37, Marc Boxerman  wrote:
>> 
>> Alexander,
>> 
>> The build still failed using fink -l build openmpi.  I’m not sure what you 
>> mean by the output getting “swallowed” but the build output went to stdout 
>> as well as to the log file.  I’m attaching the log file for your review. 
>> 
>> Thanks for your continued assistance.
>> 
>> Marc
>> 
> 
> By “swallowed”  I mean: “overwritten and lost”, e.g. due to something trying 
> to be cute with control characters.
> 
> I’ll generate a log file here and do a diff.
> 
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> 

I had a log file from yesterday’s test.  I found the issue, I think.  There was 
indeed an earlier error:

./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_fstype.lo] Error 128
make[4]: *** Waiting for unfinished jobs
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_iread_fake.lo] Error 128
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_opencoll_scalable.lo] Error 128
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_subarray.lo] Error 129
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_write_nolock.lo] Error 128
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_write_coll.lo] Error 128
make[4]: *** [Makefile:3396: adio/common/ad_write_str_naive.lo] Error 129
./libtool: fork: Resource temporarily unavailable
make[4]: *** [Makefile:3396: adio/common/ad_iwrite_fake.lo] Error 129
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
./libtool: fork: Resource temporarily unavailable
 
:   error: Failed to create 'adio/common/.libs'
make[4]: *** [Makefile:3396: adio/common/ad_iwrite.lo] Error 1

OS X has a fairly ungenerous default number of processes and number of files 
that it allows a user to open, so the build might well be triggering that, 
particularly if you’re using your system for other stuff.  

Fortunately, there are a few options:

1)  This version of openmpi is currently available in the 10.11 binary 
distribution.

2)  If you really want a local build, try it at a point in time where you don’t 
have a lot of other files/processes open.  Logging out or rebooting 

3)  CAUTION:   Modify the limits.  This involves mucking around in the system 
area, however.  Anyway, if you’re feeling bold, here’s a link:  
http://blog.dekstroza.io/ulimit-shenanigans-on-osx-el-capitan/  .  Note that I 
haven’t tried the method myself, because my usual solution when I want a local 
build and forking won’t work is to do option #2 and do a build when I don’t 
need the machine.

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


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Re: [Fink-beginners] Openmpi fails to build

[Alexander Hansen]

> On Nov 21, 2016, at 22:37, Marc Boxerman  wrote:
> 
> Alexander,
> 
> The build still failed using fink -l build openmpi.  I’m not sure what you 
> mean by the output getting “swallowed” but the build output went to stdout as 
> well as to the log file.  I’m attaching the log file for your review. 
> 
> Thanks for your continued assistance.
> 
> Marc
> 

By “swallowed”  I mean: “overwritten and lost”, e.g. due to something trying to 
be cute with control characters.

I’ll generate a log file here and do a diff.

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


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Re: [Fink-beginners] Openmpi fails to build

[Alexander Hansen]

> On Nov 21, 2016, at 08:31, Alexander Hansen  
> wrote:
> 
> 
>> On Nov 20, 2016, at 21:49, Marc Boxerman  wrote:
>> 
>> Alexander,
>> 
>> I had a feeling the packages could not be built separately.
>> 
>> I’m using Xcode 8.1.  But as you know, I’m not able to install the newest 
>> version of command line tools because I’m not on 10.12.  My version of 
>> command line tools is 7.3.1.0.1.1461711523.
>> 
>> Marc
>> 
> 
> Yup.  Just wanted to make sure that we attempt to reproduce the issue with 
> the same toolset. :-)
> 
> -- 
> Alexander Hansen, Ph.D.
> Fink User Liaison
> 

Unfortunately, the build failed to fail for me with 10.11/XCode CLI 7.3.1.  

One last thing to try might be to log the build via “fink -l build openmpi” 
with one build job to see if that avoids the output getting swallowed.  Also, 
if that doesn’t work, you can send me that build log and I can compare it with 
one from my setup.

-- 
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
 

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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