[gmx-users] mpi installation problems

[Carsten Kutzner]

Hi Ryan,

you need to use mpiicc instead of mpicc (should be present
also in /opt/intel/mpi/3.1/bin64/).

Carsten
  

On Jul 28, 2010, at 11:32 PM, Ryan S Davis (rsdavis1) wrote:

> I am trying to install gromacs with MPI enabled on a cluster but it seems like fftw is giving me trouble.
> 
> First, I compile everything without MPI just fine. FFTW is already on the cluster. I export pertinent variables...
> 
> export CPPFLAGS=-I/opt/fftw/3.2.1/include 
> export LDFLAGS=-L/opt/fftw/3.2.1/lib 
> export CC=/opt/intel/Compiler/11.1/069/bin/intel64/icc
> export F77=/opt/intel/Compiler/11.1/069/bin/intel64/ifort
> 
> I have been using gromacs without MPI for over a month without any issues. Now, I need to recompile mdrun with MPI. So I use...
> 
> export MPICC=/opt/intel/mpi/3.1/bin64/mpicc
> 
> 
> in addition to all the previous exports. Then, I issue the command...
> 
>> ./configure --prefix=/home/username/gromacs --enable-mpi --program-suffix=_mpi --disable-nice --enable-double
> 
> 
> which runs fine. Then I issue...
> 
>> make mdrun
> 
> and I end up with a bunch of undefined references. I am copying some of the output here. Also, I do not know if FFTW is compiled with single/double because of unresponsive admins, but I have tried compiling gromacs with both options and still got errors. Also, from a previous post, I read the idea to install FFTW with shared libraries enabled, which I tried but just ended up with other errors. Thanks in advance for any help. I have been at this for weeks.
> 
> By the way, this might not be critical, but here is some system info
> # 2 Nodes Share:
>    * 1x 1702 Altus Server (1U, contains 2 Independent Motherboards)
> # 1x AMD Dual Opteron 2380(Shanghai) 2.5GHz Quad Core (8 Cores)
> # 250GB SATA2 Hard Drive
> 
> *****output from "make mdrun" ******
> 
> /opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x649): more undefined references to `_inte
> l_fast_memcpy' follow
> /opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o): In function `apply_toms513':
> vrank3-transpose.c:(.text+0xe3e): undefined reference to `_intel_fast_memset'
> vrank3-transpose.c:(.text+0xef4): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0xf0e): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x106d): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x108a): undefined reference to `_intel_fast_memcpy'
> vrank3-transpose.c:(.text+0x110d): undefined reference to `_intel_fast_memcpy'
> /opt/fftw/3.2.1/lib/libfftw3.a(vrank3-transpose.o):vrank3-transpose.c:(.text+0x1122): more undefined references to `_int
> el_fast_memcpy' follow
> /opt/fftw/3.2.1/lib/libfftw3.a(dht-rader.o): In function `apply':
> dht-rader.c:(.text+0x4a8): undefined reference to `_intel_fast_memset'
> /opt/fftw/3.2.1/lib/libfftw3.a(dht-rader.o): In function `awake':
> dht-rader.c:(.text+0xaab): undefined reference to `_intel_fast_memset'
> /opt/fftw/3.2.1/lib/libfftw3.a(cpy1d.o): In function `fftw_cpy1d':
> cpy1d.c:(.text+0x268): undefined reference to `_intel_fast_memcpy'
> /opt/fftw/3.2.1/lib/libfftw3.a(cpy2d.o): In function `dotile_buf':
> cpy2d.c:(.text+0x6a7): undefined reference to `_intel_fast_memcpy'
> cpy2d.c:(.text+0x129f): undefined reference to `_intel_fast_memcpy'
> cpy2d.c:(.text+0x1870): undefined reference to `_intel_fast_memcpy'
> cpy2d.c:(.text+0x1902): undefined reference to `_intel_fast_memcpy'
> /opt/fftw/3.2.1/lib/libfftw3.a(cpy2d.o):cpy2d.c:(.text+0x22dd): more undefined references to `_intel_fast_memcpy' follow
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Unpack_external'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_get_errhandler'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_start'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_test'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_spawn'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Request_get_status'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPIR_Err_return_comm'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_dup'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_get_group'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_spawn_multiple'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Free_mem'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPIR_Grequest_set_lang_f77'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_create_keyval'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `b_use_gettimeofday'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_get_attr'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Close_port'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_create_errhandler'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Query_thread'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_match_size'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Open_port'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_set_attr'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_fence'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPID_Wtick'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_set_errhandler'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPIR_Err_create_code'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_set_name'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Grequest_complete'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Add_error_class'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_delete_attr'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Accumulate'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_create_hindexed'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Alltoallw'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_create_errhandler'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `MPI_F_STATUSES_IGNORE'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Win_post'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_get_attr'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Add_error_code'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_call_errhandler'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Type_get_extent'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Publish_name'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Comm_disconnect'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Get'
> /opt/intel/impi/3.1/lib64/libmpigf.so: undefined reference to `PMPI_Unpublish_name'
> --
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--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne