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--- cluster:172 [2018/08/22 12:13]
hmeij07 [Nvidia]
+++ cluster:172 [2018/08/22 19:17]
hmeij07 [Amber]
@@ Line 21: / Line 21: @@
   * install other software as regular user
 ==== Nvidia ====
+** Installation **
 <code>
@@ Line 31: / 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 gcc-gfortran-devel
+yum install gcc gcc-devel gcc-gfortran gcc-c++
 # download runfiles from https://developer.nvidia.com/cuda-downloads
@@ Line 118: / Line 120: @@
   Device2 = Tesla K20m, Device3 = Tesla K20m
 Result = PASS
+</code>
+** BandWithTest **
+<code>
+[root@n37 cuda-9.2]# /usr/local/cuda/extras/demo_suite/bandwidthTest
+[CUDA Bandwidth Test] - Starting...
+Running on...
+ Device 0: Tesla K20m
+ Quick Mode
+ Host to Device Bandwidth, 1 Device(s)
+ PINNED Memory Transfers
+   Transfer Size (Bytes)        Bandwidth(MB/s)
+   33554432                     6181.3
+ Device to Host Bandwidth, 1 Device(s)
+ PINNED Memory Transfers
+   Transfer Size (Bytes)        Bandwidth(MB/s)
+   33554432                     6530.0
+ Device to Device Bandwidth, 1 Device(s)
+ PINNED Memory Transfers
+   Transfer Size (Bytes)        Bandwidth(MB/s)
+   33554432                     137200.1
+Result = PASS
+</code>
+** Finish **
+  * yum install freeglut-devel libX11-devel libXi-devel libXmu-devel \ make mesa-libGLU-devel
+  * check for /usr/lib64/libvdpau_nvidia.so
+  * [root@n37 /]# tar -cvf /tmp/n37.chroot.ul.tar usr/local
+  * [root@n37 /]# scp /tmp/n37.chroot.ul.tar sms_server:/var/chroots/goldimages/
+==== Amber ====
+** Requirements **
+<code>
+# As root check requirements
+rpm -qa | grep ^gcc
+rpm -qa | grep ^g++
+rpm -qa | grep ^flex
+rpm -qa | grep ^tcsh
+rpm -qa | grep ^zlib
+rpm -qa | grep ^zlib-devel
+rpm -qa | grep ^bzip2
+rpm -qa | grep ^bzip2-devel
+rpm -qa | grep ^bzip
+rpm -qa | grep ^bzip-devel
+rpm -qa | grep ^libXt
+rpm -qa | grep ^libXext
+rpm -qa | grep ^libXdmcp
+rpm -qa | grep ^tkinter # weird one need python 2.6.6_something
+rpm -qa | grep ^openmpi
+rpm -qa | grep ^perl | egrep "^perl-5|^perl-ExtUtils-MakeMaker" # both
+rpm -qa | grep ^patch
+rpm -qa | grep ^bison
+# As root install missing
+yum install flex bzip2-devel libXdmcp zlib zlib-devel
+yum install tkinter openmpi perl-ExtUtils-MakeMaker patch bison
+</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
 </code>
 \\
 **[[cluster:0|Back]]**

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