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cluster:172 [2018/08/22 13:46]
hmeij07 [Nvidia] 		cluster:172 [2018/08/22 19:39]
hmeij07 [Amber]
Line 160: Line 160:
   * [root@n37 /]# scp /tmp/n37.chroot.ul.tar sms_server:/var/chroots/goldimages/   * [root@n37 /]# scp /tmp/n37.chroot.ul.tar sms_server:/var/chroots/goldimages/
  
-==== Amber 16 ====+==== Amber ==== 
 + 
 +** Requirements **
  
 <code> <code>
Line 188: Line 190:
  
 </code> </code>
 + 
 +** Compilations **
  
 +<code>
 +
 +# as regular user
 +# amber16 dir will be created
 +cd /usr/local
 +tar xvfj /share/apps/src/n33/AmberTools17.tar.bz2
 +tar xvfj /share/apps/src/n33/Amber16.tar.bz2 
 +export AMBERHOME=/usr/local/amber16
 +cd $AMBERHOME
 +
 +# to preserve existing work flows
 +export PATH=/share/apps/CENTOS6/python/2.7.9/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/python/2.7.9/lib:$LD_LIBRARY_PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/openmpi/1.8.4/lib/:$LD_LIBRARY_PATH
 +export PATH=/share/apps/CENTOS6/openmpi/1.8.4/bin:$PATH
 +
 +# use gnu, Y to patches, Y to miniconda 
 +# bundled netcdf, fftw
 +./configure gnu | tee -a  amber16-install.log 2>&1
 +source /usr/local/amber16/amber.sh
 +make install | tee -a  amber16-install.log 2>&1
 +Installation of Amber16 (serial) is complete at Wed Aug 22 10:12:55 EDT 2018.
 +
 +./configure -mpi gnu | tee -a  amber16-install.log 2>&1
 +source /usr/local/amber16/amber.sh
 +make install | tee -a amber16-install.log 2>&1
 +Installation of Amber16 (parallel) is complete at Wed Aug 22 10:36:45 EDT 2018.
 +
 +export PATH=/usr/local/cuda/bin:/usr/local/cuda/jre/bin:/usr/local/cuda/nvvm/bin:$PATH
 +export LD_LIBRARY_PATH=/usr/local/cuda/lib64:/usr/local/cuda/jre/lib:$LD_LIBRARY_PATH
 +# $AMBERHOME/AmberTools/src/configure2 
 +# edit and bypass cuda test for 9.0 -> 9.2 version
 +# please be sure to verify any results against known outcomes
 +export CUDA_HOME=/usr/local/cuda
 +./configure -cuda gnu | tee -a  amber16-install.log 2>&1 
 +source /usr/local/amber16/amber.sh
 +make install | tee -a amber16-install.log 2>&1
 +Installation of pmemd.cuda complete
 +
 +</code>
 \\ \\
 **[[cluster:0|Back]]** **[[cluster:0|Back]]**
cluster/172.txt · Last modified: 2020/07/15 17:52 by hmeij07

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