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--- cluster:172 [2018/08/23 14:02]
hmeij07 [Gromacs]
+++ cluster:172 [2018/09/25 13:57]
hmeij07 [Finish]
@@ Line 20: / Line 20: @@
   * unmount NFS mounts while installing nvidia as root
   * install other software as regular user
-  *
 ==== Nvidia ====
@@ Line 34: / 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-c++
+yum install gcc gcc-gfortran gcc-c++  # CHROOT done
 # download runfiles from https://developer.nvidia.com/cuda-downloads
-sh cuda_name_of_runfile
+# files in /usr/local/src
-sh cuda_name_of_runfile_patch
+sh cuda_9.2.148_396.37_linux.run
 Install NVIDIA Accelerated Graphics Driver for Linux-x86_64 396.26?
@@ Line 55: / Line 55: @@
 (y)es/(n)o/(q)uit: n
-#/etc/modprobe.d/blacklist-nouveau.conf, reboot before driver instllation
+# /etc/modprobe.d/blacklist-nouveau.conf (new file by nvidia)
+# reboot before driver installation # CHROOT done
 blacklist nouveau
 options nouveau modeset=0
@@ Line 61: / Line 62: @@
 # nvidia driver
-./cuda_name_of_runfile -silent -driver
+./cuda_name_of_runfile \-\-silent \-\-accept-eula driver
 # backup
@@ Line 72: / Line 73: @@
 [root@n37 src]# find /usr/local/cuda-9.2 -name nvidia-xconfig*
 [root@n37 src]#
-[root@n37 src]# scp n78:/etc/X11/xorg.conf /etc/X11/
+[root@n37 src]# scp n78:/etc/X11/xorg.conf /etc/X11/  # CHROOT done
 # Device files/dev/nvidia* exist with 0666 permissions?
@@ Line 80: / Line 81: @@
 # new kernel initramfs, load
 dracut --force
+# for mapd graphics support needs to be enabled
+nvidia-smi --gom=0
+# have left persistence and exclusivity at defaults for now
 reboot
@@ Line 157: / Line 163: @@
 ** Finish **
-  * yum install freeglut-devel libX11-devel libXi-devel libXmu-devel \ make mesa-libGLU-devel
+  * yum install freeglut-devel libX11-devel libXi-devel libXmu-devel \ make mesa-libGLU-devel # CHROOT done
   * check for /usr/lib64/libvdpau_nvidia.so
   * [root@n37 /]# tar -cvf /tmp/n37.chroot.ul.tar usr/local
@@ Line 167: / Line 173: @@
 <code>
-# As root check requirements
+# As root check requirements # CHROOT done
 rpm -qa | grep ^gcc
 rpm -qa | grep ^g++
@@ Line 187: / Line 193: @@
 rpm -qa | grep ^bison
-# As root install missing
+# As root install missing # CHROOT done
 yum install flex bzip2-devel libXdmcp zlib zlib-devel
 yum install tkinter openmpi perl-ExtUtils-MakeMaker patch bison
@@ Line 274: / Line 280: @@
 As root install
-  * yum install cmake
+  * cmake, latest version, never understand why so far ahead of distro...
 Download and extract source. Using same environment as Amber compilation.
+<code>
+ cd gromacs-2018/
+ mkdir build
+ cd build
+ which mpicc mpicxx
+/share/apps/CENTOS6/openmpi/1.8.4/bin/mpicc
+/share/apps/CENTOS6/openmpi/1.8.4/bin/mpicxx
+ CC=mpicc CXX=mpicxx \
+   /share/apps/CENTOS7/cmake/3.12.1/bin/cmake .. \
+  -DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018 \
+  -DGMX_BUILD_OWN_FFTW=ON -DGMX_MPI=ON -DGMX_GPU=ON
+ CC=mpicc CXX=mpicxx make
+ CC=mpicc CXX=mpicxx make install
+</code>
 ==== Lammps ====
 As root install
-  * yum install libjpeg libjpeg-devel libjpeg-turbo libjpeg-turbo-devel
+  * yum install libjpeg libjpeg-devel libjpeg-turbo libjpeg-turbo-devel # CHROOT done
-  * yum install blas blas-devel lapack lapack-devel boost boost-devel
+  * yum install blas blas-devel lapack lapack-devel boost boost-devel # CHROOT done
 For Lammps-22Aug18 I followed the top installation instructions at this page
@@ Line 291: / Line 317: @@
   * to stay with openmpi-1.8.4 (not mpich3...)
-  * consulting the ARCH web page I choose -arch=sm_35
+  * consulting the ARCH web page I choose -arch=sm_35 (on n37 for K20)
-Good thing we're doing this now, future versions of CUDA will not support the K20s anymore. In fact on that web site they are not mentioned, only the K40/K80 gpus. So we'll see what testing reveals.  Please double check results against previous runs. Compile as regular user and stage lmp_mpi in /usr/local/lammps-22Aug10/lmp-mpi-presision1precision2-with-cuda...
+Good thing we're doing this now, future versions of CUDA will not support the K20s anymore. In fact on that web site they are not mentioned, only the K40/K80 gpus. So we'll see what testing reveals.  Please double check results against previous runs. Compile as regular user and stage lmp_mpi in /usr/local/lammps-22Aug18/
 <code>
@@ Line 299: / Line 325: @@
 [hmeij@n37 src]$ ll /usr/local/lammps-22Aug18/
 total 104356
--rwxr-xr-x 1 hmeij its 35739800 Aug 23 08:49 lmp_mpi-double-double-with-cuda
+-rwxr-xr-x 1 hmeij its 35739800 Aug 23 08:49 lmp_mpi-double-double-with-gpu
--rwxr-xr-x 1 hmeij its 35555672 Aug 23 09:11 lmp_mpi-single-double-with-cuda
+-rwxr-xr-x 1 hmeij its 35555672 Aug 23 09:11 lmp_mpi-single-double-with-gpu
--rwxr-xr-x 1 hmeij its 35559552 Aug 23 09:53 lmp_mpi-single-single-with-cuda
+-rwxr-xr-x 1 hmeij its 35559552 Aug 23 09:53 lmp_mpi-single-single-with-gpu
 </code>
 ==== mapd ====
+  * https://www.mapd.com/docs/latest/4_centos7-yum-gpu-ce-recipe.html
+<code>
+useradd -U mapd
+# mapd.repo
+[mapd-ce-cuda]
+name=mapd ce - cuda
+baseurl=https://releases.mapd.com/ce/yum/stable/cuda
+gpgcheck=1
+gpgkey=https://releases.mapd.com/GPG-KEY-mapd
+yum  install \
+  copy-jdk-configs java-1.8.0-openjdk-headless \
+  javapackages-tools libxslt \
+  lksctp-tools python-javapackages \
+  python-lxml tzdata-java  # CHROOT done
+yum install mapd   # n37:/usr/local/src
+# User specific aliases and functions
+export MAPD_USER=mapd
+export MAPD_GROUP=mapd
+export MAPD_STORAGE=/var/lib/mapd
+export MAPD_PATH=/opt/mapd
+# The $MAPD_STORAGE directory must be dedicated to MapD
+</code>
+==== Finish ====
+  * Make the final tar file for /usr/local and post with CHROOT # done
+  * Install all the packages of this page in CHROOT # marked done
+To do another node, the steps are
+  * add node in deploy.txtof n37.chroot/
+  * ./deploy.txt `grep node_name deploy.txt`
+  * scp in place passwd, shadow, group, hosts, fstab from global archive
+  * umount -a
+  * ONBOOT=no, ib0 ??? connectX mlx4_0 IB interface breaks in CentOS 7.3+
+  * bootlocal=EXIT then reboot then check polkit user … screws up systemd-logind
+  * hostnamectl set-hostname node_name (logout/login)
+  * tar in place n37.chroot.ul.tar.gz in / FIRST
+  * REMOVE /usr/local/cuda-9.2 then uplink eth1 install kernel-devel
+  * Nvidia install: files in /usr/local/src
+    * sh cuda_name_of_runfile
+    * nvidia-modprobe.sh
 \\
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