Re: Myrinet and MPI question

From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Thu Jul 22 2004 - 11:49:07 CDT

Maybe it is because you put the -lpthread at the wrong place (CXXFLAGS)
which never passed to link time. Add those to namd2 link comamnd should
fix it.

Gengbin

Brian Bennion wrote:

>My best guess here
>
>Try just -pthread ie remove the l
>
>
>
>On Thu, 22 Jul 2004, Hrant Gharabekyan wrote:
>
>
>
>>I compiled charm ++
>>./build charm++ mpi-linux gm --basedir /opt/mpich-gm-1.2.5-12/
>>builded normalyy, megatest passed normally for 4 nodes.
>>
>>Configuring Namd ./config tcl fftw Linux-i686-MPI
>>When I trying compile Namd 2.5 without any changes in makefile
>>output is :
>>/home/sicnas/Hrant/Namd/TCL/lib/libtcl8.3.a(tclUnixPipe.o)(.text+0xe2): In function `TclpCreateTempFile':
>>: the use of `tmpnam' is dangerous, better use `mkstemp'
>>/opt/mpich-gm-1.2.5-12/lib/libmpich.a(gmpi_malloc.o)(.text+0x64): In function `malloc_atfork':
>>: undefined reference to `pthread_self'
>>/opt/mpich-gm-1.2.5-12/lib/libmpich.a(gmpi_malloc.o)(.text+0xcf): In function `malloc_atfork':
>>: undefined reference to `pthread_mutex_lock'
>>/opt/mpich-gm-1.2.5-12/lib/libmpich.a(gmpi_malloc.o)(.text+0xd7): In function `malloc_atfork':
>>: undefined reference to `pthread_mutex_unlock'
>>/opt/mpich-gm-1.2.5-12/lib/libmpich.a(gmpi_malloc.o)(.text+0x135): In function `free_atfork':
>>: undefined reference to `pthread_self'
>>/opt/mpich-gm-1.2.5-12/lib/libmpich.a(gmpi_malloc.o)(.text+0x152): In function `free_atfork':
>>: undefined reference to `pthread_mutex_lock'
>>.....
>>exit with error.
>>
>>I tryed changes in makefile (but in wiki writed that that changes for
>>GM 2), in all cases I tryed.
>>CXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) -lpthread
>>output is same.
>>
>>I read in wiki there writen
>>--with-device=ch_gm:-disable-registration when configuring MPICH-GM
>>but my MPICH-GM already installed, and I haven't any possibility to
>>change it.
>>
>>Is there any possible solution for my problem.
>>
>>A lot of Thank's
>>
>>Hrant
>>
>>
>>
>>
>
>*****************************************************************
>**Brian Bennion, Ph.D. **
>**Computational and Systems Biology Division **
>**Biology and Biotechnology Research Program **
>**Lawrence Livermore National Laboratory **
>**P.O. Box 808, L-448 bennion1_at_llnl.gov **
>**7000 East Avenue phone: (925) 422-5722 **
>**Livermore, CA 94550 fax: (925) 424-6605 **
>*****************************************************************
>
>

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