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--- cluster:172 [2018/08/22 13:45]
hmeij07 [Amber 16]
+++ cluster:172 [2018/08/22 19:39]
hmeij07 [Amber]
@@ Line 33: / Line 33: @@
 yum update kernel kernel-tools kernel-tools-libs
 yum install kernel-devel kernel-headers (remove old headers after reboot)
-yum install gcc gcc-devel gcc-gfortran
+yum install gcc gcc-devel gcc-gfortran gcc-c++
 # download runfiles from https://developer.nvidia.com/cuda-downloads
@@ Line 160: / Line 160: @@
   * [root@n37 /]# scp /tmp/n37.chroot.ul.tar sms_server:/var/chroots/goldimages/
-==== Amber 16 ====
+==== Amber ====
+** Requirements **
 <code>
@@ Line 188: / Line 190: @@
 </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]]**

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