Differences

This shows you the differences between two versions of the page.

--- cluster:172 [2018/08/22 12:00]
hmeij07 [Note]
+++ cluster:172 [2018/08/22 15:05]
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 84: / Line 86: @@
   * export PATH=/usr/local/cuda/bin:$PATH
   * export LD_LIBRARY_PATH=/usr/local/cuda/lib64:$LD_LIBRARY_PATH
+**Verification**
+<code>
+[root@n37 cuda-9.2]# /usr/local/cuda/extras/demo_suite/deviceQuery
+/usr/local/cuda/extras/demo_suite/deviceQuery Starting...
+ CUDA Device Query (Runtime API) version (CUDART static linking)
+Detected 4 CUDA Capable device(s)
+Device 0: "Tesla K20m"
+  CUDA Driver Version / Runtime Version          9.2 / 9.2
+  CUDA Capability Major/Minor version number:    3.5
+...
+> Peer access from Tesla K20m (GPU0) -> Tesla K20m (GPU1) : Yes
+> Peer access from Tesla K20m (GPU0) -> Tesla K20m (GPU2) : No
+> Peer access from Tesla K20m (GPU0) -> Tesla K20m (GPU3) : No
+> Peer access from Tesla K20m (GPU1) -> Tesla K20m (GPU0) : Yes
+> Peer access from Tesla K20m (GPU1) -> Tesla K20m (GPU2) : No
+> Peer access from Tesla K20m (GPU1) -> Tesla K20m (GPU3) : No
+> Peer access from Tesla K20m (GPU2) -> Tesla K20m (GPU0) : No
+> Peer access from Tesla K20m (GPU2) -> Tesla K20m (GPU1) : No
+> Peer access from Tesla K20m (GPU2) -> Tesla K20m (GPU3) : Yes
+> Peer access from Tesla K20m (GPU3) -> Tesla K20m (GPU0) : No
+> Peer access from Tesla K20m (GPU3) -> Tesla K20m (GPU1) : No
+> Peer access from Tesla K20m (GPU3) -> Tesla K20m (GPU2) : Yes
+deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 9.2,
+  CUDA Runtime Version = 9.2, NumDevs = 4,
+  Device0 = Tesla K20m, Device1 = Tesla K20m,
+  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 fix test for 9.0 -> 9,2 version
+export CUDA_HOME=/usr/local/cuda
+./configure -cuda gnu | tee -a  amber16-install.log 2>&1
+</code>
 \\
 **[[cluster:0|Back]]**

DokuWiki

User Tools

Site Tools

Differences

Page Tools