AMBER Archive (2009)

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

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Fri Jul 24 2009 - 20:24:10 CDT

Dear Mengjuei Hsieh,
 
Thanks for your detailed suggestion first. I am so glad that I have get it down after I set the right path of MPI_HOME as /usr/local/amber10. The problem is mainly because I point the MPI_HOME as /usr/local/amber10/bin, but it is wrong according to your this mail which you just set ~/amber10. I really appreciate for your useful help, I don't know which words could express my gratitude.
 
By the way, why I got nothing after I run "rpm -qa | grep -i openmpi"? I could not understand that.
 
All in all, thank you once again.
 
Best wishes to you!
 
Qinghua

________________________________
From: Mengjuei Hsieh <mjhsieh_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Saturday, July 25, 2009 2:12:00 AM
Subject: Re: 回复： [AMBER] errors of PMEMD installation

Qinghua,

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. 

-- 
Mengjuei

On Fri, Jul 24, 2009 at 2:18 AM, Qinghua Liao<fantasticqhl_at_yahoo.com> 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<fantasticqhl_at_yahoo..com> 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=$LD_LIBRARY_PATH:/usr/local/lib
> source /opt/intel/fc/9.0/bin/ifortvars..sh ia32
> source /opt/intel/cc/9.0/bin/iccvars.sh ia32
> export FC=/opt/intel/fc/9.0/bin/ifort
> export CC=/opt/intel/cc/9.0/bin/icc
> export CXX=/opt/intel/cc/9.0/bin/icpc
> export MKL_HOME=/opt/intel/mkl/9.0
> export LD_LIBRARY_PATH=$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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