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Subject: Re: [OMPI devel] Open MPI (not quite) on Cray XC30
From: Paul Hargrove (phhargrove_at_[hidden])
Date: 2013-01-25 17:13:41


Still having problems on the Cray XC30, but now they are when linking an
MPI app:

$ ./INSTALL/bin/mpicc -o ring_c examples/ring_c.c
> fs_lustre_file_open.c:(.text+0x130): undefined reference to
> `llapi_file_create'
> fs_lustre_file_open.c:(.text+0x17e): undefined reference to
> `llapi_file_get_stripe'
> /usr/bin/ld: link errors found, deleting executable `ring_c'
> collect2: error: ld returned 1 exit status

It appears that lustre support was found at configure time using a test
that used "-llustre -llusterapi":

> configure:157666: checking if possible to link LUSTRE
> configure:157680: cc -std=gnu99 -o conftest -O3 -DNDEBUG
> -finline-functions -fno-strict-aliasing -fexceptions -D_REENTRANT
> -I/global/homes/h/hargrove/GSCRATCH/OMPI/openmpi-1.9a1r27905/opal/mca/hwloc/hwloc151/hwloc/include
> -I/global/homes/h/hargrove/GSCRATCH/OMPI/openmpi-1.9a1r27905/BUILD-edison/opal/mca/hwloc/hwloc151/hwloc/include
> -I/global/homes/h/hargrove/GSCRATCH/OMPI/openmpi-1.9a1r27905/opal/mca/event/libevent2019/libevent
> -I/global/homes/h/hargrove/GSCRATCH/OMPI/openmpi-1.9a1r27905/opal/mca/event/libevent2019/libevent/include
> -I/global/homes/h/hargrove/GSCRATCH/OMPI/openmpi-1.9a1r27905/BUILD-edison/opal/mca/event/libevent2019/libevent/include
> -I/opt/cray/pmi/default/include -I/opt/cray/pmi/default/include
> -I/opt/cray/pmi/default/include -I/opt/cray/pmi/default/include
> -I/usr//include/lustre/ -fexceptions -L/usr//lib64 conftest.c -lnsl
> -lutil -lnsl -lutil -llustre -llustreapi

However, those two libs are NOT included when linking an MPI application:

> $ ./INSTALL/bin/mpicc -o ring_c examples/ring_c.c -v 2>&1 | grep collect
> /opt/gcc/4.7.2/snos/libexec/gcc/x86_64-suse-linux/4.7.2/collect2
> --sysroot= -m elf_x86_64 -static -o ring_c -u pthread_mutex_trylock -u
> pthread_mutex_destroy -u pthread_create /usr/lib/../lib64/crt1.o
> /usr/lib/../lib64/crti.o
> /opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/crtbeginT.o
> -L/opt/cray/pmi/default/lib64 -L/opt/cray/alps/default/lib64
> -L/global/homes/h/hargrove/GSCRATCH/OMPI/openmpi-1.9a1r27905/INSTALL/lib
> -L/opt/cray/udreg/2.3.2-1.0500.5931.3.1.ari/lib64
> -L/opt/cray/ugni/4.0-1.0500.5836.7.58.ari/lib64
> -L/opt/cray/pmi/4.0.0-1.0000.9282.69.4.ari/lib64
> -L/opt/cray/dmapp/4.0.1-1.0500.5932.6.5.ari/lib64
> -L/opt/cray/xpmem/0.1-2.0500.36799.3.6.ari/lib64
> -L/opt/cray/alps/5.0.1-2.0500.7663.1.1.ari/lib64
> -L/opt/cray/rca/1.0.0-2.0500.37705.3.12.ari/lib64
> -L/opt/cray/mpt/5.6.0/gni/mpich2-gnu/47/lib
> -L/opt/cray/mpt/5.6.0/gni/sma/lib64
> -L/opt/cray/libsci/12.0.00/gnu/47/sandybridge/lib
> -L/opt/cray/alps/5.0.1-2.0500.7663.1.1.ari/lib64
> -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2
> -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../../../lib64
> -L/lib/../lib64 -L/usr/lib/../lib64
> -L/opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/../../..
> /scratch1/scratchdirs/hargrove/cceRJNtp.o -lmpi -lpmi -lalpslli -lalpsutil
> -lnsl -lutil -lnsl -lutil -lopen-rte -lpmi -lalpslli -lalpsutil -lnsl
> -lutil -lnsl -lutil -lopen-pal -lpmi -lalpslli -lalpsutil -lnsl -lutil
> -lnsl -lutil -lrca -L/opt/cray/atp/1.6.0/lib/ --undefined=_ATP_Data_Globals
> --undefined=__atpHandlerInstall -lAtpSigHCommData -lAtpSigHandler
> --start-group -lgfortran -lscicpp_gnu -lsci_gnu_mp -lstdc++ -lgfortran
> -lmpich_gnu_47 -lmpl -lrt -lsma -lxpmem -ldmapp -lugni -lpmi -lalpslli
> -lalpsutil -lalps -ludreg -lpthread -lm --end-group -lgomp -lpthread
> --start-group -lgcc -lgcc_eh -lc --end-group
> /opt/gcc/4.7.2/snos/lib/gcc/x86_64-suse-linux/4.7.2/crtend.o
> /usr/lib/../lib64/crtn.o
> collect2: error: ld returned 1 exit status

Of course the obvious work-around to try is adding "-llustre -llustreapi"
to my command line. However, that doesn't work because mpicc places my
"-l" args BEFORE its own "-lmpi". Since "-static" is also among the
arguments, no symbols are picked up from the luster libs when they appear
on the command line before "-lmpi", from which lustre symbols are
referenced.

Best guess(es):
EITHER config/ompi_check_lustre.m4 is failing to add "-llustre -llustreapi"
to some variable
OR the variable set by config/ompi_check_lustre.m4 isn't making its way
into the application link command for some reason

Note that this is a --disable-shared/--enable-static build which may differ
from other systems where LUSTRE support gets used/tested.

-Paul

On Fri, Jan 25, 2013 at 12:01 PM, Ralph Castain <rhc_at_[hidden]> wrote:

> Thanks Paul
>
> I'm currently tracking down a problem on the Cray XE6 - it appears that
> recent OS release changed the way alps stores allocation info :-(
>
> Will hopefully have it running soon.
>
> On Jan 25, 2013, at 10:50 AM, Paul Hargrove <phhargrove_at_[hidden]> wrote:
>
> I was able to compile with openmpi-1.9a1r27905.tar.bz
>
> I'll report again when I've had an opportunity to run something like
> ring_c.
>
> Thanks,
> -Paul
>
>
> On Tue, Jan 22, 2013 at 6:08 PM, Ralph Castain <rhc_at_[hidden]> wrote:
>
>> I went ahead and removed the duplicate code, so this should work now. The
>> problem is that we re-factored the ompi_info/orte-info code, but didn't
>> complete the job - specifically, the orte-info tool didn't get updated.
>> It's about to get revamped yet again when the ompi-rte branch gets
>> committed to the trunk, so I'd rather not do any more with it now.
>>
>> Hopefully, this will be the minimum required.
>>
>>
>> On Jan 22, 2013, at 4:20 PM, Paul Hargrove <phhargrove_at_[hidden]> wrote:
>>
>> I am using the openmpi-1.9a1r27886 tarball and I still see an error for
>> one of the two duplicate symbols:
>>
>> CCLD orte-info
>> ../../../orte/.libs/libopen-rte.a(orte_info_support.o): In function
>> `orte_info_show_orte_version':
>> ../../orte/runtime/orte_info_support.c:(.text+0xe10): multiple definition
>> of `orte_info_show_orte_version'
>> version.o:../../../../orte/tools/orte-info/version.c:(.text+0x2370):
>> first defined here
>>
>> -Paul
>>
>>
>> On Fri, Jan 18, 2013 at 3:52 AM, George Bosilca <bosilca_at_[hidden]>wrote:
>>
>>> Luckily for us all the definitions contain the same constant (orte).
>>> r27864 should fix this.
>>>
>>> George.
>>>
>>>
>>> On Jan 18, 2013, at 06:21 , Paul Hargrove <PHHargrove_at_[hidden]> wrote:
>>>
>>> My employer has a nice new Cray XC30 (aka Cascade), and I thought I'd
>>> give Open MPI a quick test.
>>>
>>> Given that it is INTENDED to be API-compatible with the XE series, I
>>> began configuring with
>>> CC=cc CXX=CC FC=ftn --with-platform=lanl/cray_xe6/optimized-nopanasas
>>> However, since this is Intel h/w, I commented-out the following 2 lines
>>> in the platform file:
>>> with_wrapper_cflags="-march=amdfam10"
>>> CFLAGS=-march=amdfam10
>>>
>>> I am using PrgEnv-gnu/5.0.15, though PrgEnv-intel is the default on our
>>> system
>>>
>>> As far as I know, use of 1.6.x is out - no ugni at all, right?
>>> So, I didn't even try.
>>>
>>> I gave openmpi-1.7rc6 a try, but the ALPS headers and libs have moved
>>> (as mentioned in ompi-trunk/config/orte_check_alps.m4).
>>> Perhaps one should CMR the updated-for-CLE-5 configure logic to the 1.7
>>> branch?
>>>
>>> Next, I tried a trunk nightly tarball: openmpi-1.9a1r27862.tar.bz2
>>> As I mentioned above, the trunk has the right logic for locating ALPS.
>>> However, it looks like there is some untested code, protected by "#if
>>> WANT_CRAY_PMI2_EXT", that needs work:
>>>
>>> make[2]: Entering directory
>>> `/global/scratch/sd/hargrove/OMPI/openmpi-1.9a1r27862/BUILD/orte/mca/db/pmi'
>>> CC db_pmi_component.lo
>>> CC db_pmi.lo
>>> ../../../../../orte/mca/db/pmi/db_pmi.c: In function 'store':
>>> ../../../../../orte/mca/db/pmi/db_pmi.c:202: error: 'ptr' undeclared
>>> (first use in this function)
>>> ../../../../../orte/mca/db/pmi/db_pmi.c:202: error: (Each undeclared
>>> identifier is reported only once
>>> ../../../../../orte/mca/db/pmi/db_pmi.c:202: error: for each function it
>>> appears in.)
>>> make[2]: *** [db_pmi.lo] Error 1
>>> make[2]: Leaving directory
>>> `/global/scratch/sd/hargrove/OMPI/openmpi-1.9a1r27862/BUILD/orte/mca/db/pmi'
>>> make[1]: *** [all-recursive] Error 1
>>> make[1]: Leaving directory
>>> `/global/scratch/sd/hargrove/OMPI/openmpi-1.9a1r27862/BUILD/orte'
>>> make: *** [all-recursive] Error 1
>>>
>>> I added the missing "char *ptr" declaration a few lines before it's
>>> first use, and resumed the build.
>>> This time the build terminated at
>>>
>>> make[2]: Entering directory
>>> `/global/scratch/sd/hargrove/OMPI/openmpi-1.9a1r27862/BUILD/opal/tools/wrappers'
>>> CC opal_wrapper.o
>>> CCLD opal_wrapper
>>> /usr/bin/ld: attempted static link of dynamic object
>>> `../../../opal/.libs/libopen-pal.so'
>>> collect2: error: ld returned 1 exit status
>>>
>>> So I went back to the platform file and changed
>>> enable_shared=yes
>>> to
>>> enable_shared=no
>>> No big deal there - I had to make the same change for our XE6.
>>>
>>> And so I started back at configure (after a "make distclean", to be
>>> safe), and here is the next error:
>>>
>>> Making all in tools/orte-info
>>> make[2]: Entering directory
>>> `/global/scratch/sd/hargrove/OMPI/openmpi-1.9a1r27862/BUILD/orte/tools/orte-info'
>>> CCLD orte-info
>>> ../../../orte/.libs/libopen-rte.a(orte_info_support.o): In function
>>> `orte_info_show_orte_version':
>>> orte_info_support.c:(.text+0xd70): multiple definition of
>>> `orte_info_show_orte_version'
>>> version.o:version.c:(.text+0x4b0): first defined here
>>> ../../../orte/.libs/libopen-rte.a(orte_info_support.o):(.data+0x0):
>>> multiple definition of `orte_info_type_orte'
>>> orte-info.o:(.data+0x10): first defined here
>>> /usr/bin/ld: link errors found, deleting executable `orte-info'
>>> collect2: error: ld returned 1 exit status
>>> make[2]: *** [orte-info] Error 1
>>>
>>> I am not sure how to fix this, but I would guess this is probably a
>>> simple fix for somebody who knows OMPI's build infrastructure better than I.
>>>
>>> -Paul
>>>
>>> --
>>> Paul H. Hargrove PHHargrove_at_[hidden]
>>> Future Technologies Group
>>> Computer and Data Sciences Department Tel: +1-510-495-2352
>>> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900
>>> _______________________________________________
>>> devel mailing list
>>> devel_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>>
>>>
>>>
>>> _______________________________________________
>>> devel mailing list
>>> devel_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>>
>>
>>
>>
>> --
>> Paul H. Hargrove PHHargrove_at_[hidden]
>> Future Technologies Group
>> Computer and Data Sciences Department Tel: +1-510-495-2352
>> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900
>> _______________________________________________
>> devel mailing list
>> devel_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>
>>
>>
>> _______________________________________________
>> devel mailing list
>> devel_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>
>
>
>
> --
> Paul H. Hargrove PHHargrove_at_[hidden]
> Future Technologies Group
> Computer and Data Sciences Department Tel: +1-510-495-2352
> Lawrence Berkeley National Laboratory Fax: +1-510-486-6900
> _______________________________________________
> devel mailing list
> devel_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>
>
>
> _______________________________________________
> devel mailing list
> devel_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>

-- 
Paul H. Hargrove                          PHHargrove_at_[hidden]
Future Technologies Group
Computer and Data Sciences Department     Tel: +1-510-495-2352
Lawrence Berkeley National Laboratory     Fax: +1-510-486-6900