Skip to Content.
Sympa Menu

charm - Re: [charm] [ppl] Install charm++ on Cray XE/XK

charm AT lists.cs.illinois.edu

Subject: Charm++ parallel programming system

List archive

Re: [charm] [ppl] Install charm++ on Cray XE/XK


Chronological Thread 
  • From: Phil Miller <mille121 AT illinois.edu>
  • To: Bo Zhang <zhang416 AT indiana.edu>
  • Cc: "charm AT cs.uiuc.edu" <charm AT cs.uiuc.edu>
  • Subject: Re: [charm] [ppl] Install charm++ on Cray XE/XK
  • Date: Thu, 29 Aug 2013 14:55:35 -0500
  • List-archive: <http://lists.cs.uiuc.edu/pipermail/charm/>
  • List-id: CHARM parallel programming system <charm.cs.uiuc.edu>

You just tried to run a Cray compute-node binary on the login/head
node. You need to submit a job, and run the binary using aprun, just
like you would any other program on that system.

On Thu, Aug 29, 2013 at 2:54 PM, Bo Zhang
<zhang416 AT indiana.edu>
wrote:
> Phil,
>
> I downloaded the 6.5.1 released version and built it with
>
> './build charm++ gemini_gni-crayxe smp persistent hugepages -j16
> --with-production'
>
> And I got the following error this time.
>
> zhang416@login1:~/charm-6.5.1/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello>
> make
> ../../../bin/charmc hello.ci
> ../../../bin/charmc -c hello.C
> ../../../bin/charmc -language charm++ -o hello hello.o
> ../../../bin/../lib/libconv-util.a(sockRoutines.o): In function
> `skt_lookup_ip':
> sockRoutines.c:(.text+0x3a3): warning: Using 'gethostbyname' in statically
> linked applications requires at runtime the shared libraries from the glibc
> version used for linking
> zhang416@login1:~/charm-6.5.1/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello>
> ./hello
> libhugetlbfs [login1:38222]: WARNING: No mount point found for default huge
> page size. Using first available mount point.
> libhugetlbfs [login1:38222]: WARNING: Hugepage size 2097152
> unavailablelibhugetlbfs [login1:38222]: WARNING: Hugepage size 2097152
> unavailableSegmentation fault
>
> I am sorry to bother you this much. I thank you very much for helping me
> with this.
>
> Bo
>
> P.S. :
>
> Currently Loaded Modulefiles:
> 1) modules/3.2.6.7 18)
> csa/3.0.0-1_2.0401.37452.4.50.gem
> 2) eswrap/1.0.20-1.010101.433.0 19)
> job/1.5.5-0.1_2.0401.35380.1.10.gem
> 3) craype-network-gemini 20)
> xpmem/0.1-2.0401.36790.4.3.gem
> 4) PrgEnv-gnu/4.1.40 21)
> gni-headers/2.1-1.0401.5675.4.4.gem
> 5) atp/1.6.3 22)
> dmapp/3.2.1-1.0401.5983.4.5.gem
> 6) xe-sysroot/4.1.40 23)
> pmi/4.0.1-1.0000.9421.73.3.gem
> 7) switch/1.0-1.0401.36779.2.72.gem 24)
> ugni/4.0-1.0401.5928.9.5.gem
> 8) shared-root/1.0-1.0401.37253.3.50.gem 25)
> udreg/2.3.2-1.0401.5929.3.3.gem
> 9) pdsh/2.26-1.0401.37449.1.1.gem 26) xt-libsci/12.1.01
> 10) nodehealth/5.0-1.0401.38460.12.18.gem 27) gcc/4.8.1
> 11) lbcd/2.1-1.0401.35360.1.2.gem 28) xt-asyncpe/5.22
> 12) hosts/1.0-1.0401.35364.1.115.gem 29) craype-interlagos
> 13) configuration/1.0-1.0401.35391.1.2.gem 30) cray-mpich/6.0.1
> 14) ccm/2.2.0-1.0401.37254.2.142 31) moab/7.2.3
> 15) audit/1.0.0-1.0401.37969.2.32.gem 32) torque/4.2.3.1
> 16) rca/1.0.0-2.0401.38656.2.2.gem 33) craype-hugepages8M
> 17) dvs/1.8.6_0.9.0-1.0401.1401.1.120
>
>
>
>
> On Aug 29, 2013, at 3:25 PM, Phil Miller wrote:
>
> I just pushed the fix for the 'undefined reference to assert' error.
> If you wish to continue using the development version, please pull and
> rebuild.
>
> As Jim mentioned, it may be easier to simply use the released version
> of Charm++ instead.
>
> On Thu, Aug 29, 2013 at 2:09 PM, Phil Miller
> <mille121 AT illinois.edu>
> wrote:
>
> The undefined references to 'assert' are the result of a recent
>
> change, that will be fixed quickly.
>
>
> On Thu, Aug 29, 2013 at 2:07 PM, Bo Zhang
> <zhang416 AT indiana.edu>
> wrote:
>
> Hello Jim,
>
>
> I swap and load the modules as you suggested. And I rebuilt the package
>
> several times:
>
>
> Thu Aug 29 14:18:14 EDT 2013
>
> Using the following build command:
>
> ./build charm++ gemini_gni-crayxe craycc hugepages -j16
>
> --with-production
>
>
> Thu Aug 29 14:48:27 EDT 2013
>
> Using the following build command:
>
> ./build charm++ gemini_gni-crayxe craycc smp persistent hugepages -j16
>
> --with-production
>
>
> Thu Aug 29 14:59:20 EDT 2013
>
> Using the following build command:
>
> ./build charm++ gemini_gni-crayxe smp persistent hugepages -j16
>
> --with-production
>
>
> Each time, the built was successful. But I still cannot make the
>
> simplesayhello example. For the last set of build options I used, I got the
>
> following the messages:
>
>
> zhang416@login1:~/repository/charm/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello>
>
> make
>
> ../../../bin/charmc hello.ci
>
> ../../../bin/charmc -c hello.C
>
> ../../../bin/charmc -language charm++ -o hello hello.o
>
> ../../../bin/../lib/libconv-util.a(sockRoutines.o): In function
>
> `skt_lookup_ip':
>
> sockRoutines.c:(.text+0x3a3): warning: Using 'gethostbyname' in statically
>
> linked applications requires at runtime the shared libraries from the glibc
>
> version used for linking
>
> ../../../bin/../lib/libconv-util.a(persist-comm.o): In function
>
> `compressFloatingPoint':
>
> persist-comm.c:(.text+0x2f3): undefined reference to `assert'
>
> ../../../bin/../lib/libconv-util.a(persist-comm.o): In function
>
> `compressDouble':
>
> persist-comm.c:(.text+0x451): undefined reference to `assert'
>
> collect2: error: ld returned 1 exit status
>
> Fatal Error by charmc in directory
>
> /N/u/zhang416/BigRed2/repository/charm/gemini_gni-crayxe-hugepages-persistent-smp/tests/charm++/simplearrayhello
>
> Command CC -I/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/include
>
> -I/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/include
>
> -I/opt/cray-hss-devel/7.0.0/include
>
> -I/opt/cray/krca/1.0.0-2.0401.36792.3.70.gem/include
>
> -I/opt/cray/gni-headers/2.1-1.0401.5675.4.4.gem/include
>
> -I/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/include -D_REENTRANT -rdynamic -o
>
> hello -L../../../bin/../lib -I../../../bin/../include
>
> ../../../bin/../lib/libldb-rand.o hello.o moduleinit22274.o
>
> ../../../bin/../lib/libmemory-default.o
>
> ../../../bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y
>
> -lconv-core -lconv-util ../../../bin/../lib/custom_partitioner.o -lckqt
>
> -lpthread -lrt -lz -ldl -lm returned error code 1
>
> charmc exiting...
>
> make: *** [hello] Error 1
>
>
> I look forward to hearing further instructions from you. Thank you.
>
>
> Bo
>
>
>
>
> On Aug 29, 2013, at 2:30 PM, Jim Phillips wrote:
>
>
>
> For NAMD we use these modules:
>
>
> module swap PrgEnv-cray PrgEnv-gnu
>
> module load rca
>
> module load craype-hugepages8M
>
>
> And these sets of options:
>
>
> gemini_gni-crayxe hugepages persistent
>
>
> gemini_gni-crayxe hugepages persistent smp
>
>
> -Jim
>
>
>
> On Thu, 29 Aug 2013, Phil Miller wrote:
>
>
> Going on what I can remember and intuit from what I see here, you may
>
>
> need to add the build option 'hugepages' to your build command. You
>
>
> should also ensure that you have one of the craype-hugepages* modules
>
>
> loaded.
>
>
>
> I'm not sure why this error appeared though, and will check with the
>
>
> rest of the team on how we can prevent it in the future.
>
>
>
> Thanks, and I hope that helps
>
>
>
> Phil
>
>
>
> On Thu, Aug 29, 2013 at 12:59 PM, Bo Zhang
> <zhang416 AT indiana.edu>
> wrote:
>
>
> Dear developing team:
>
>
>
> This is Bo Zhang from Indiana University. I am trying to install charm++
>
>
> locally on a Cray XE6/XK7 machine. The build command used is:
>
>
>
> './build charm++ gemini_gni-crayxe craycc -j16 --with-production'
>
>
>
> After running the command, it shows that charm++ was built successfully.
>
>
> Next, I followed the suggestion to try the sample program
>
>
> 'gemini_gni-crayxe-craycc/tests/charm++/simplearrayhello', but the make was
>
>
> terminated with error.
>
>
>
> zhang416@login1:~/repository/charm/tests/charm++/simplearrayhello>
> make
>
>
> ../../../bin/charmc hello.ci
>
>
> ../../../bin/charmc -c hello.C
>
>
> ../../../bin/charmc -language charm++ -o hello hello.o
>
>
> /opt/cray/xe-sysroot/4.1.40/usr/lib64/libhugetlbfs.a(hugeutils.o): In
>
>
> function `gethugepagesize':
>
>
> /usr/src/packages/BUILD/cray-libhugetlbfs-2.11/hugeutils.c:863: multiple
>
>
> definition of `gethugepagesize'
>
>
> ../../../bin/../lib/cray_tlbhack.o:(.text+0x0): first defined here
>
>
> /opt/cray/xe-sysroot/4.1.40/usr/lib64/libpthread.a(sem_open.o): In function
>
>
> `sem_open':
>
>
> /usr/src/packages/BUILD/glibc-2.11.3/nptl/sem_open.c:333: warning: the use
>
>
> of `mktemp' is dangerous, better use `mkstemp'
>
>
> ../../../bin/../lib/libconv-util.a(sockRoutines.o): In function
>
>
> `skt_lookup_ip':
>
>
> /N/hd00/zhang416/BigRed2/repository/charm/gemini_gni-crayxe-craycc/tmp/sockRoutines.c:295:
>
>
> warning: Using 'gethostbyname' in statically linked applications requires at
>
>
> runtime the shared libraries from the glibc version used for linking
>
>
> Fatal Error by charmc in directory
>
>
> /N/u/zhang416/BigRed2/repository/charm/tests/charm++/simplearrayhello
>
>
> Command CC -I/opt/cray/rca/1.0.0-2.0401.38656.2.2.gem/include
>
>
> -I/opt/cray/pmi/4.0.1-1.0000.9421.73.3.gem/include
>
>
> -I/opt/cray-hss-devel/7.0.0/include
>
>
> -I/opt/cray/krca/1.0.0-2.0401.36792.3.70.gem/include
>
>
> -I/opt/cray/gni-headers/2.1-1.0401.5675.4.4.gem/include
>
>
> -I/opt/cray/ugni/4.0-1.0401.5928.9.5.gem/include -o hello
>
>
> -L../../../bin/../lib -I../../../bin/../include
>
>
> ../../../bin/../lib/libldb-rand.o hello.o moduleinit44124.o
>
>
> ../../../bin/../lib/libmemory-default.o
>
>
> ../../../bin/../lib/libthreads-default.o -lckmain -lck -lconv-cplus-y
>
>
> -lconv-core -lconv-util ../../../bin/../lib/custom_partitioner.o -lckqt -ldl
>
>
> -lrt ../../../bin/../lib/cray_tlbhack.o -lm returned error code 1
>
>
> charmc exiting...
>
>
> make: *** [hello] Error 1
>
>
>
> Would you please let me know how to resolve this issue? Thank you very much.
>
>
>
> Sincerely,
>
>
>
> Bo
>
>
>
>
>
>
>
>
>
> _______________________________________________
>
>
> charm mailing list
>
>
> charm AT cs.uiuc.edu
>
>
> http://lists.cs.uiuc.edu/mailman/listinfo/charm
>
>
>
> _______________________________________________
>
>
> charm mailing list
>
>
> charm AT cs.uiuc.edu
>
>
> http://lists.cs.uiuc.edu/mailman/listinfo/charm
>
>
> _______________________________________________
>
>
> ppl mailing list
>
>
> ppl AT cs.uiuc.edu
>
>
> http://lists.cs.uiuc.edu/mailman/listinfo/ppl
>
>
>
>
>




Archive powered by MHonArc 2.6.16.

Top of Page