Research:pmemd tacc - Revision history

Eew947: Created page with "'''Install PMEMD on ranger (or lonestar)''' <span style="font-size: smaller;" /> === Configure ===
2025-04-21T23:30:51Z

Created page with "'''<span style="font-size: large;"><span style="font-family: Arial;">Install PMEMD on ranger (or lonestar)</span></span>''' <span style="font-size: large;"><span style="font-family: Arial;"><span style="font-size: medium;"><span style="font-size: smaller;" /></span></span></span> === <span style="font-size: larger;"><span style="font-family: Arial;">Configure</span></span> === <span style="font-size: large;"><span style="font-family: Arial;"><span style="font..."

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'''<span style="font-size: large;"><span style="font-family: Arial;">Install PMEMD on ranger (or lonestar)</span></span>'''

<span style="font-size: large;"><span style="font-family: Arial;"><span style="font-size: medium;"><span style="font-size: smaller;" /></span></span></span>

=== <span style="font-size: larger;"><span style="font-family: Arial;">Configure</span></span> ===

<span style="font-size: large;"><span style="font-family: Arial;"><span style="font-size: medium;"><span style="font-size: smaller;">1. Log on to tacc with your account.</span></span></span></span>

<span style="font-size: large;"><span style="font-family: Arial;"><span style="font-size: medium;"><span style="font-size: smaller;">2. Do "cdw" to redirect to your work directory.</span></span></span></span>

<span style="font-size: large;"><span style="font-family: Arial;"><span style="font-size: medium;"><span style="font-size: smaller;">3. Copy PMEMD directory here.</span></span></span></span>

<span style="font-size: large;"><span style="font-family: Arial;"><span style="font-size: medium;"><span style="font-size: smaller;">4. </span></span></span></span>Unload mvapich and load mvapich2 module

    module unload mvapich

    module swap pgi intel

    module load mvapich2

    module load mkl

   

    Now if you do "module list", the undated loaded modules will be displayed.

5. Go to pmemd directory and run "./configure linux64_opteron ifort mvapich"<br>

    linux64_opteron: the platform. (If you compile on lonestar, the platform is linux_emt64t)<br>

    ifort: compiler.<br>

    mvapich: parallel implementation. (Actually mvapich2, which is just loaded)<br>

    You can run ./configure without arguments to see the option list.<br>

<br>

6. You will be asked "Use Intel MKL? (better performance) (answer yes or no):"<br>

    There is some problem with MKL which needs to be fixed. For now, type "no".

<br>

7. Then you are asked "Please enter directory where mvapich mpi files are installed:"<br>

    Type: /opt/apps/intel10_1/mvapich2/1.2/

<br>

8. Now "Please enter name of directory where Infiniband libraries are installed:"

    Since mvapich is the mpi based on infiniband network, the infiniband libraries are under the same directory of mvapich2.

    So "/opt/apps/intel10_1/mvapich2/1.2/lib/"

<br>

9. A new config.h file will be generated. Open the config.h file, and add "-DAMOEBA" at the end of the line "F90_DEFINES = -DFFTLOADBAL_2PROC"

<br>

<span style="font-size: x-large;">Compile</span>

1. Go to src directory and do "make clean".

2. Do "make"

    A new pmemd executible will be generated if the compiling is successful

<br>

<br>

   

= Compile sander.MPI of AMBER10 <br> =

== Ranger ==

http://archive.ambermd.org/200808/0120.html

==Nova==
setenv AMBERHOME XXX
setenv MKL_HOME /opt/intel/mkl/8.1/lib/em64t
setenv MPI_HOME /opt/mpich2-fc13
./configure_amber -p4 -static ifort