AMBER Archive (2009)

Subject: Re: 回复: [AMBER] errors of PMEMD installation

From: Mengjuei Hsieh (
Date: Fri Jul 24 2009 - 13:12:00 CDT


The reason to use ia32 version of the compiler is that your operating
system is in 32bit.

I am not sure if openmpi could possibly interfere your PMEMD building
procedure, but a wrong MPI_HOME setting sure does. Try to make sure
that MPI_HOME is pointing to the right path of your lammpi.

Nevertheless you can try to use "rpm -qa | grep -i openmpi" to figure
out the name of the openmpi package and use "rpm -e <the package
name>" to remove the package.

Although you probably don't need too much extra information, I just
tested this on an ia32 fedora core 4 box. Here is how I built it:

         I have a clean amber10 in my ~/src/amber10, enter the directory
         of amber10/src. Then I did "env MKL_HOME=/opt/intel/mkl/8.0.1
        ./configure_amber -lamsource -p4 -nosanderidc". After that I ran
        the script of ./configure_lam. Waited a while since it costs some
        minutes to do it. Having lammpi installed in ~/src/amber10, you
        need to have your MPI_HOME environment variable pointing to the
        directory ~/src/amber10, and run the configuration in pmemd
        directory. "./configure linux_p4 ifort lam nobintraj" is what I
        did (nobintraj is not relevant). I was able to make install
        WITHOUT PROBLEM. Note that you don't have to compile your own
        lammpi, what I wanted to do is to make sure every factor is
        under my control.


On Fri, Jul 24, 2009 at 2:18 AM, Qinghua Liao<> wrote: > By the way, the compiler I use is version ia32, I don't know why you ask me that.

On Fri, Jul 24, 2009 at 2:59 AM, Qinghua Liao<> wrote: > Dear Mengjuei Hsieh, > I followed your suggestion, but it still didnot work, errors were just the same. I am just confused now and I don't know how to deal with it. The following lines are the environment I set, could you find some problem about this error? > > AMBERHOME=/usr/local/amber10 > export AMBERHOME > export PATH=$PATH:$AMBERHOME/bin > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib > source /opt/intel/fc/9.0/bin/ ia32 > source /opt/intel/cc/9.0/bin/ ia32 > export FC=/opt/intel/fc/9.0/bin/ifort > export CC=/opt/intel/cc/9.0/bin/icc > export CXX=/opt/intel/cc/9.0/bin/icpc > export MKL_HOME=/opt/intel/mkl/9.0 > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/mkl/9.0/lib/32 > > By the way, I have installed openmpi in /usr/local , and I don't know how to uninstall it after I tried to use the rpm tools. Does that interfere the compilation of PMEMD with lammpi? Or could you tell me how to uninstall openmpi? > > Thanks very much in advance! > > All the best! > > Qinghua

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