# OS: RHEL/CentOS 7.5
### openmpi + ucx 專區
### fast ucx
```bash
mpirun --allow-run-as-root --mca pml ucx --mca scoll ucx --mca atomic ucx --map-by node -x UCX_NET_DEVICES=mlx4_0:1 -np 64 -H a1:16,a2:16,b1:16,b2:16 <command to application>
```
### with GPUDirect RDMA
```bash
-x UCX_TLS=rc,sm,cuda_copy,gdr_copy,cuda_ipc
--mca btl_openib_want_cuda_gdr 1
```
### 讓 CentOS 保持在 7.5
```bash
cat > /etc/yum.repos.d/CentOS-Vault.repo <<'EOF'
# C7.5.1804
[C7.5.1804-base]
name=CentOS-7.5.1804 - Base
baseurl=http://vault.centos.org/7.5.1804/os/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
enabled=0
[C7.5.1804-updates]
name=CentOS-7.5.1804 - Updates
baseurl=http://vault.centos.org/7.5.1804/updates/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
enabled=0
[C7.5.1804-extras]
name=CentOS-7.5.1804 - Extras
baseurl=http://vault.centos.org/7.5.1804/extras/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
enabled=0
[C7.5.1804-centosplus]
name=CentOS-7.5.1804 - CentOSPlus
baseurl=http://vault.centos.org/7.5.1804/centosplus/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
enabled=0
[C7.5.1804-fasttrack]
name=CentOS-7.5.1804 - Fasttrack
baseurl=http://vault.centos.org/7.5.1804/fasttrack/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-7
enabled=0
EOF
```
```bash
yum-config-manager --disable CentOS\*
yum-config-manager --enable C7.5\*
```
### install essential
```bash
yum update -y && yum install -y mlocate git \
python3 \
bc tree svn gcc gcc-c++ \
vim net-tools wget make \
pciutils gtk2 atk cairo \
gcc-gfortran tcsh lsof \
nfs-utils automake autoconf \
tcl tcl-devel tk \
kernel-devel \
kernel-devel-$(uname -r) \
yum-utils \
device-mapper-persistent-data \
lvm2 \
openssl-devel \
libuuid-devel \
libseccomp-devel \
squashfs-tools \
alsa-lib \
gettext-devel \
libevent-devel \
python-devel \
flex \
libpsm2-devel.x86_64 \
gtk3 \
libXScrnSaver \
numactl-devel \
binutils-devel \
libudev-devel \
libxml2-devel \
xorg-x11-server-Xorg xorg-x11-xauth xorg-x11-apps \
libtool bison bison-devel \
doxygen graphviz \
bzip2 man \
libnl libmnl numactl \
libmnl tcl gcc-gfortran tk \
git \
environment-modules
```
### 添加epel repository
```
yum install -y https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm
```
### 雜項 (hostname 要重開才會變)
```bash
echo "root:0" | chpasswd
echo "export LANG=en_US.UTF-8" >> ~/.bashrc
systemctl stop firewalld
systemctl disable firewalld
hostnamectl set-hostname
mkdir /app /isc
exec bash
```
## CMake
```bash
cd /tmp
wget https://cmake.org/files/v3.11/cmake-3.11.0.tar.gz
tar vxf cmake-3.11.0.tar.gz -C /app
cd /app/cmake-3.11.0
./bootstrap --parallel=$(nproc)
make -j$(nproc)
make install -j$(nproc)
```
## infiniband
### ofed driver
```bash
cd /tmp
wget http://content.mellanox.com/ofed/MLNX_OFED-4.4-2.0.7.0/MLNX_OFED_LINUX-4.4-2.0.7.0-rhel7.5-x86_64.tgz
tar vxf MLNX_OFED_LINUX-4.4-2.0.7.0-rhel7.5-x86_64.tgz -C /app
cd /app/MLNX_OFED_LINUX-4.4-2.0.7.0-rhel7.5-x86_64
./mlnxofedinstall --all --force
/etc/init.d/openibd restart
```
### install hpcx
```bash
cd /tmp
wget http://content.mellanox.com/hpc/hpc-x/v2.4/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat7.5-x86_64.tbz
tar xvf hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat7.5-x86_64.tbz -C /app
mv /app/hpcx-v2.4.0-gcc-MLNX_OFED_LINUX-4.4-2.0.7.0-redhat7.5-x86_64 /app/hpcx
```
### rebuild openmpi with intel compiler in hpcx
```bash
cd /app/hpcx
mv ompi _ompi
export HPCX_HOME=$PWD
cd sources
tar xpf ${HPCX_HOME}/sources/openmpi-gitclone.tar.gz
cd openmpi-gitclone
module load icc
./configure CC=icc CXX=icpc F77=ifort FC=ifort --prefix=${HPCX_HOME}/ompi \
--with-hcoll=${HPCX_HOME}/hcoll --with-ucx=${HPCX_HOME}/ucx \
--with-platform=contrib/platform/mellanox/optimized --with-tm=/app/pbs \
--with-cuda=/app/cuda10.1 2>&1 | tee config-icc-output.log
make all -j$(nproc) 2>&1 | tee build_icc.log && \
make -j$(nproc) install 2>&1 | tee install_icc.log
```
#### 如果有 cuda
```bash
--with-cuda=<cuda dir>
```
#### 如果有 pbs
```bash
--with-tm=<pbs dir>
```
### hpcx modulefile
```bash
mkdir /usr/share/Modules/modulefiles/hpcx
ln -s /app/hpcx/modulefiles/hpcx /usr/share/Modules/modulefiles/hpcx/2.4.0
```
### network-ib0
```bash
vim /etc/sysconfig/network-scripts/ifcfg-ib0
```
```bash
CONNECTED_MODE=no
TYPE=InfiniBand
PROXY_METHOD=none
BROWSER_ONLY=no
BOOTPROTO=static
DEFROUTE=yes
IPV4_FAILURE_FATAL=no
IPV6INIT=yes
IPV6_AUTOCONF=yes
IPV6_DEFROUTE=yes
IPV6_FAILURE_FATAL=no
IPV6_ADDR_GEN_MODE=stable-privacy
NAME=ib0
DEVICE=ib0
ONBOOT=yes
IPADDR=10.0.0.X
NETMASK=255.255.255.0
```
```bash
systemctl restart network
```
## ib sm (在其中一台做就可以)
```bash
echo "Default=0xffff, ipoib, mtu=5, defmember=both: ALL=both;" > /etc/opensm/partitions.conf
systemctl restart opensmd
systemctl enable opensmd
```
### GCC 5.1.0, 9.3.0
## GCC-$version
```bash
export version=自己挑
cd /tmp
wget https://ftp.gnu.org/gnu/gcc/gcc-${version}/gcc-${version}.tar.gz
tar vxf gcc-${version}.tar.gz -C /app
cd /app/gcc-${version}
./contrib/download_prerequisites
mkdir build
cd build
../configure --enable-checking=release \
--enable-languages=c,c++,fortran --disable-multilib \
--prefix=/usr/local/gcc-${version}
make -j$(nproc)
make install -j$(nproc)
mkdir /usr/share/Modules/modulefiles/gcc
cat > /usr/share/Modules/modulefiles/gcc/${version} <<EOF
#%Module
set TOP_DIR /usr/local/gcc-${version}
prepend-path PATH \${TOP_DIR}/bin
prepend-path LD_LIBRARY_PATH \${TOP_DIR}/lib64
EOF
```
## Intel
:::warning
與下面 psxe_runtime 擇一安裝
:::
### Intel psxe 2019.5
#### obtain psxe
```bash
cd /tmp
wget http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/15809/parallel_studio_xe_2019_update5_cluster_edition_online.tgz
tar xvf parallel_studio_xe_2019_update5_cluster_edition_online.tgz -C /app
```
#### configure silent.cfg
```bash
cd /app/parallel_studio_xe_2019_update5_cluster_edition_online
sed -i 's/ACCEPT_EULA=decline/ACCEPT_EULA=accept/' silent.cfg
sed -i 's/#ACTIVATION_SERIAL_NUMBER=snpat/ACTIVATION_SERIAL_NUMBER=S477-Z28VJXXB/' silent.cfg
sed -i 's/ACTIVATION_TYPE=exist_lic/ACTIVATION_TYPE=serial_number/' silent.cfg
```
#### install psxe
```
./install.sh -s silent.cfg
```
#### 小調整 (只能做一次)
```bash
sed -i '133d;134d;135d;136d;137d' /opt/intel/compilers_and_libraries_2019.5.281/linux/bin/compilervars.sh
```
#### psxe module file
```bash
cd /app
git clone https://git.code.sf.net/p/env2/code env2-code
mkdir /usr/share/Modules/modulefiles/icc
mkdir /usr/share/Modules/modulefiles/mkl
mkdir /usr/share/Modules/modulefiles/impi
echo "#%Module" > /usr/share/Modules/modulefiles/icc/2019.5.281
perl /app/env2-code/env2 -from bash -to modulecmd \
"/opt/intel/compilers_and_libraries_2019.5.281/linux/bin/compilervars.sh intel64" >> /usr/share/Modules/modulefiles/icc/2019.5.281
echo "#%Module" > /usr/share/Modules/modulefiles/mkl/2019.5.281
perl /app/env2-code/env2 -from bash -to modulecmd \
"/opt/intel/compilers_and_libraries_2019.5.281/linux/mkl/bin/mklvars.sh intel64" >> /usr/share/Modules/modulefiles/mkl/2019.5.281
echo "#%Module" > /usr/share/Modules/modulefiles/impi/2019.5.281
perl /app/env2-code/env2 -from bash -to modulecmd \
"/opt/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/bin/mpivars.sh" >> /usr/share/Modules/modulefiles/impi/2019.5.281
```
### Intel psxe 2018.4
#### obtain psxe
```bash
cd /tmp
wget http://registrationcenter-download.intel.com/akdlm/irc_nas/tec/13717/parallel_studio_xe_2018_update4_cluster_edition_online.tgz
tar xvf parallel_studio_xe_2018_update4_cluster_edition_online.tgz -C /app
```
#### configure silent.cfg
```bash
cd /app/parallel_studio_xe_2018_update4_cluster_edition_online
sed -i 's/ACCEPT_EULA=decline/ACCEPT_EULA=accept/' silent.cfg
sed -i 's/#ACTIVATION_SERIAL_NUMBER=snpat/ACTIVATION_SERIAL_NUMBER=S477-Z28VJXXB/' silent.cfg
sed -i 's/ACTIVATION_TYPE=exist_lic/ACTIVATION_TYPE=serial_number/' silent.cfg
```
#### install psxe
```
./install.sh -s silent.cfg
```
#### 小調整 (只能做一次)
```bash
sed -i '121d;122d;123d;124d' /opt/intel/compilers_and_libraries_2018.5.274/linux/bin/compilervars.sh
```
#### psxe module file
```bash
echo "#%Module" > /usr/share/Modules/modulefiles/icc/2018.5.274
perl /app/env2-code/env2 -from bash -to modulecmd \
"/opt/intel/compilers_and_libraries_2018.5.274/linux/bin/compilervars.sh intel64" >> /usr/share/Modules/modulefiles/icc/2018.5.274
echo "#%Module" > /usr/share/Modules/modulefiles/mkl/2018.5.274
perl /app/env2-code/env2 -from bash -to modulecmd \
"/opt/intel/compilers_and_libraries_2018.5.274/linux/mkl/bin/mklvars.sh intel64" >> /usr/share/Modules/modulefiles/mkl/2018.5.274
echo "#%Module" > /usr/share/Modules/modulefiles/impi/2018.5.274
perl /app/env2-code/env2 -from bash -to modulecmd \
"/opt/intel/compilers_and_libraries_2018.5.274/linux/mpi/intel64/bin/mpivars.sh" >> /usr/share/Modules/modulefiles/impi/2018.5.274
```
## Intel Runtime: 只 for 跑程式
:::warning
與上面 psxe 擇一安裝
:::
### obtain psxe_runtime repo
```
yum-config-manager --add-repo https://yum.repos.intel.com/2018/setup/intel-psxe-runtime-2018.reposudo yum-config-manager --add-repo https://yum.repos.intel.com/2018/setup/intel-psxe-runtime-2018.repo
rpm --import https://yum.repos.intel.com/2018/setup/RPM-GPG-KEY-intel-psxe-runtime-2018
```
### install components (可自選)
- 從<a href="https://software.intel.com/en-us/articles/installing-intel-parallel-studio-xe-runtime-2020-using-yum-repository">這裡</a>看有什麼可以選
```
yum install -y intel-icc-runtime-64bit-2018.4-274.x86_64 \
intel-ifort-runtime-64bit-2018.4-274.x86_64 \
intel-mkl-runtime-64bit-2018.4-274.x86_64 \
intel-mpi-runtime-64bit-2018.4-274.x86_64
```
### env variables
```
source /opt/intel/psxe_runtime/linux/bin/psxevars.sh
```
## hostfile
```bash
vim /etc/hosts
127.0.0.1 localhost localhost.localdomain localhost4 localhost4.localdomain4
::1 localhost localhost.localdomain localhost6 localhost6.localdomain6
10.0.0.1 a1
10.0.0.2 a2
10.0.0.3 b1
10.0.0.4 b2
```
## 互串
```bash
ssh-keygen -t rsa -N '' -f ~/.ssh/id_rsa
ssh-copy-id root@a1
ssh-copy-id root@a2
ssh-copy-id root@b1
ssh-copy-id root@b2
```
### 設定ssh捨棄knownhost
```
cat > ~/.ssh/config <<EOF
StrictHostKeyChecking=no
UserKnownHostsFile=/dev/null
EOF
```
## GPU
### blacklist nouveau
```bash
vim /etc/modprobe.d/blacklist-nouveau.conf
blacklist nouveau
options nouveau modeset=0
dracut --force
```
### CUDA 10.1
```bash
cd /tmp
wget https://developer.nvidia.com/compute/cuda/10.1/Prod/local_installers/cuda_10.1.105_418.39_linux.run
sh cuda_10.1.105_418.39_linux.run
** 然後就開始 GUI 操作嚕 **
```
### CUDA 10.2
```bash
wget http://developer.download.nvidia.com/compute/cuda/10.2/Prod/local_installers/cuda-repo-rhel7-10-2-local-10.2.89-440.33.01-1.0-1.x86_64.rpm
rpm -ivh cuda-repo-rhel7-10-2-local-10.2.89-440.33.01-1.0-1.x86_64.rpm
yum clean all
yum install -y dkms
yum install -y nvidia-driver-latest-dkms cuda
yum install -y cuda-drivers
```
### CUDA 10.0
```bash
wget -O cuda_10.0.130_410.48_linux.run https://developer.nvidia.com/compute/cuda/10.0/Prod/local_installers/cuda_10.0.130_410.48_linux
sh cuda_10.0.130_410.48_linux.run \
--silent --toolkit --verbose
```
### modulefile
```bash
mkdir /usr/share/Modules/modulefiles/cuda
vim /usr/share/Modules/modulefiles/cuda/10.2
#%Module
conflict cuda
set CUDA_PATH /usr/local/cuda-10.2
setenv CUDA_DIR ${CUDA_PATH}
prepend-path PATH ${CUDA_PATH}/bin
prepend-path LD_LIBRARY_PATH ${CUDA_PATH}/lib64
prepend-path CPATH ${CUDA_PATH}/include
vim /usr/share/Modules/modulefiles/cuda/10.0
#%Module
conflict cuda
set CUDA_PATH /usr/local/cuda-10.0
setenv CUDA_DIR ${CUDA_PATH}
prepend-path PATH ${CUDA_PATH}/bin
prepend-path LD_LIBRARY_PATH ${CUDA_PATH}/lib64
prepend-path CPATH ${CUDA_PATH}/include
```
### env variable(for openmpi)
```bash
echo "module load cuda/10.0" >> ~/.bashrc
```
### reboot
```bash
reboot
```
## mpich (option)
### obtain mpich
```
wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz
```
### install mpich
```
tar xvf mpich-3.3.2.tar.gz
cd mpich-3.3.2
./configure --prefix=/app/mpich
make -j16
make install -j16
```
### create mpich modulefile
```
mkdir /usr/share/Modules/modulefiles/mpich
vim /usr/share/Modules/modulefiles/mpich/3.3.2
#%Module
conflict intel
set TOP_DIR /app/mpich
prepend-path PATH ${TOP_DIR}/bin
prepend-path LD_LIBRARY_PATH ${TOP_DIR}/lib
prepend-path MANPATH ${TOP_DIR}/share/man
```
## openmpi (option)
### install openmpi
```bash
cd /tmp
wget https://download.open-mpi.org/release/open-mpi/v3.1/openmpi-3.1.5.tar.gz
tar xvf openmpi-3.1.5.tar.gz -C /app
cd /app/openmpi-3.1.5
module purge
module load cuda/10.0
./configure --with-cuda --prefix=/app/openmpi-3.1.5
make -j4
make install -j4
```
### create openmpi modulefile
```bash
mkdir /usr/share/Modules/modulefiles/openmpi
vim /usr/share/Modules/modulefiles/openmpi/3.1.5
#%Module
conflict intel
set TOP_DIR /app/openmpi-3.1.5
prepend-path PATH ${TOP_DIR}/bin
prepend-path LD_LIBRARY_PATH ${TOP_DIR}/lib
prepend-path MANPATH ${TOP_DIR}/share/man
```
## HPL <img src="https://i.imgur.com/NJh8F1B.jpg" width=50px>
### obtain hpl-2.0_FERMI_v15
```bash
wget -O hpl-2.0_FERMI_v15.tar 34.80.90.52:8090/upload/2019/10/hpl-2.0_FERMI_v15-d12aaaa9505945cdbfb1ee1c2d5d8a32.tar
tar xvf hpl-2.0_FERMI_v15.tar -C /app
```
### configure Make.CUDA
```bash
cd /app/hpl-2.0_FERMI_v15
vim Make.CUDA
TOPdir = /app/hpl-2.0_FERMI_v15
MPdir = /app/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64
MPinc = -I$(MPdir)/include
MPlib = $(MPdir)/lib/release/libmpi.so
LAdir = /app/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64
LAinc = -I$(LAdir)/../../include
CC = mpiicc
CCFLAGS = $(HPL_DEFS) -fomit-frame-pointer -O3 -funroll-loops -W -Wall -fopenmp -std=c99
LINKER = $(CC)
```
### make
```bash
module purge
module load intel cuda/10.0
make arch=CUDA -j4
```
### HPL.dat
```bash
cd bin/CUDA
vim HPL.dat
```
HPL.dat :
```bash
HPLinpack benchmark input file
Innovative Computing Laboratory, University of Tennessee
HPL.out output file name (if any)
6 device out (6=stdout,7=stderr,file)
1 # of problems sizes (N)
50000 Ns
1 # of NBs
256 NBs
0 PMAP process mapping (0=Row-,1=Column-major)
1 # of process grids (P x Q)
1 Ps
2 Qs
16.0 threshold
1 # of panel fact
0 1 2 PFACTs (0=left, 1=Crout, 2=Right)
1 # of recursive stopping criterium
2 8 NBMINs (>= 1)
1 # of panels in recursion
2 NDIVs
1 # of recursive panel fact.
0 1 2 RFACTs (0=left, 1=Crout, 2=Right)
1 # of broadcast
0 2 BCASTs (0=1rg,1=1rM,2=2rg,3=2rM,4=Lng,5=LnM)
1 # of lookahead depth
1 0 DEPTHs (>=0)
1 SWAP (0=bin-exch,1=long,2=mix)
192 swapping threshold
1 L1 in (0=transposed,1=no-transposed) form
1 U in (0=transposed,1=no-transposed) form
1 Equilibration (0=no,1=yes)
8 memory alignment in double (> 0)
```
### run_linpack
```bash
vim run_linpack
HPL_DIR=/app/hpl-2.0_FERMI_v15
mpirun -np 2 -ppn 1 -f ~/hosts $HPL_DIR/bin/CUDA/xhpl
```
### run hpl
```bash
module purge
module load intel cuda/10.0
./run_linpack
```
## HPCG <img src="https://i.imgur.com/NJh8F1B.jpg" width=50px>
### obtain HPCG
```bash
wget http://www.hpcg-benchmark.org/downloads/hpcg-3.1_cuda-10_ompi-3.1_gcc485_sm_35_sm_50_sm_60_sm_70_sm75_ver_10_9_18.tgz
tar vxf hpcg-3.1_cuda-10_ompi-3.1_gcc485_sm_35_sm_50_sm_60_sm_70_sm75_ver_10_9_18.tgz -C /app
```
### HPL.dat
```bash
cd /app/hpcg-3.1_cuda-10_ompi-3.1_gcc485_sm_35_sm_50_sm_60_sm_70_sm75_ver_10_9_18
vim hpcg.dat
#調整參數
```
### run HPCG
```bash
module purge
module load openmpi cuda/10.0
mpirun --allow-run-as-root --prefix /app/openmpi -np 2 --host ib1,ib2 ./xhpcg-3.1_gcc_485_cuda-10.0.130_ompi-3.1.0_sm_35_sm_50_sm_60_sm_70_sm_75_ver_10_9_18
```
## HPCC <img src="https://i.imgur.com/ntqP33x.png" width=50px>
### obtain hpcc-1.5.0
```bash
wget http://icl.cs.utk.edu/projectsfiles/hpcc/download/hpcc-1.5.0.tar.gz
tar xvf hpcc-1.5.0.tar.gz -C /app
```
### configure Make.Linux_ATHLON_CBLAS
```bash
cd /app/hpcc-1.5.0/hpl
cp setup/Make.Linux_ATHLON_CBLAS .
vim Make.Linux_ATHLON_CBLAS
TOPdir = /app/hpcc-1.5.0/hpl
MPdir = /app/intel/compilers_and_libraries_2020.0.166/linux/mpi/intel64
MPinc = -I$(MPdir)/include
MPlib = $(MPdir)/lib/release/libmpi.so
LAdir = /app/intel/compilers_and_libraries_2020.0.166/linux/mkl/lib/intel64
LAinc = -I$(LAdir)/../../include
LAlib = -L$(LAdir) -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
CC = mpiicc
CCFLAGS = $(HPL_DEFS) -fomit-frame-pointer -O3 -funroll-loops -W -Wall -std=c99
```
### make
```bash
cd ..
module purge
module load intel
make arch=Linux_ATHLON_CBLAS -j4
```
### run hpcc
```bash
cp _hpccinf.txt hpccinf.txt
vim hpccinf.txt
#調整 P, Q, NB....
mpirun -np 8 -f ~/hosts ./hpcc
```
## Elmer/Ice <img src="https://i.imgur.com/ntqP33x.png" width=50px>
### obtain elmer
```bash
git clone https://www.github.com/ElmerCSC/elmerfem
```
### make elmer builddir
```bash
cd elmerfem
mkdir builddir
cd builddir
```
### create build sciprt
```bash
vim build.sh
```
<p>build.sh :</p>
```bash
#!/bin/bash
CMAKE=cmake
# Installation directory
TIMESTAMP=$(date +"%m-%d-%y")
ELMER_REV="Elmer_devel_${TIMESTAMP}"
ELMERSRC="/root/elmerfem"
BUILDDIR="$ELMERSRC/builddir"
IDIR="/usr/local/$ELMER_REV"
cd ${BUILDDIR}
module purge
module load intel/2019.10.24
$CMAKE $ELMERSRC \
-DCMAKE_INSTALL_PREFIX=$IDIR \
-DCMAKE_C_COMPILER=mpiicc \
-DCMAKE_CXX_COMPILER=mpiicpc \
-DCMAKE_Fortran_COMPILER=mpiifort \
-DWITH_MPI:BOOL=TRUE \
-DWITH_ElmerIce:BOOL=TRUE
make -j4 && make install
rm /usr/local/Elmer-devel
ln -s $IDIR /usr/local/Elmer-devel
```
### build elmer/ice
```bash
source build.sh
```
### modulefile
```bash
mkdir /usr/share/Modules/modulefiles/elmer
vim /usr/share/Modules/modulefiles/elmer/1.0
#%Module
prepend-path PATH /usr/local/Elmer-devel/bin
```
### obtain LID3D
```bash
cd
wget https://hpcadvisorycouncil.atlassian.net/wiki/download/attachments/1169784836/LID3D.tgz
tar xvf LID3D.tgz
```
### test LID3D_20k with 8 process
```bash
cd LID3D
module purge
module load intel
module load elmer
ElmerGrid 2 2 LID3D_extrude_20k/ -metiskway 8
mpirun -np 8 -f ~/hosts ElmerSolver
```
## NFS
### **Type 1: NFS over Ethernet**
```
mkdir /nfs
chmod 777 /nfs
```
#### server端 (n11)
```
vim /etc/exports
/nfs *(rw,sync,no_root_squash,no_all_squash)
```
#### client端
```
mount -t nfs n11:/nfs /nfs
```
### **Type 2: NFS over RDMA**
```
mkdir /nfs-rdma
chmod 777 /nfs-rdma
```
#### server端 (IB1)
```
vim /etc/rdma/rdma.conf
SVCRDMA_LOAD=yes
vim /etc/sysconfig/nfs
RPCNFSDARGS="--rdma=20049"
echo rdma 20049 > /proc/fs/nfsd/portlist
vi /etc/exports
/nfs-rdma *(rw,sync,no_root_squash,no_all_squash)
```
#### client端
```
vim /etc/rdma/rdma.conf
XPRTRDMA_LOAD=yes
mount -t nfs -o proto=rdma,port=20049 IB1:/nfs-rdma /nfs-rdma
```
### **Type 3: NFS over ZFS over Ethernet**
#### 磁區設定
##### 檢查/dev/sda4
```
parted -l
```
##### 若/dev/sda4的Type為extended
```
fdisk /dev/sda
m(查看命令)
d(delete)
4
n(new)
p(primary)
enter
enter
w(write)
reboot
```
#### install zfs
##### CentOS
```
yum install -y epel-release
yum --enablerepo=epel install -y dkms
yum install -y http://download.zfsonlinux.org/epel/zfs-release.el7_7.noarch.rpm
yum install -y zfs
yum remove -y zfs zfs-kmod spl spl-kmod libzfs2 libnvpair1 libuutil1 libzpool2 zfs-release
yum install -y http://download.zfsonlinux.org/epel/zfs-release.el7_7.noarch.rpm
yum autoremove -y
yum clean metadata
yum install -y zfs
```
#### configure zfs
##### module
```
modprobe zfs
```
##### create pool
```
zpool create -f zdisk1 /dev/sda4
```
##### 檢查zfs的service, 確保為enable
```
systemctl status zfs.target
```
#### 卸載module
```
module unload <name>
```
#### 查看MODULEPATH上的module
```
module avail
```
#### 查看loaded module
```
module list
```
## 有用軟體
### tshark
#### install tshark
```
yum install -y wireshark
```
#### run tshark
```
tshark -i <interface> -w <output-file>
```
#### non-root user
##### root端設定
```
usermod -aG wireshark t1
setcap cap_net_raw,cap_net_admin=eip /usr/sbin/dumpcap
```
### ibdump
```
wget https://linux.mellanox.com/public/repo/mlnx_ofed/4.7-1.0.0.1/rhel7.7/x86_64/MLNX_LIBS/ibdump-5.0.0-3.47100.x86_64.rpm
rpm -iv ibdump-5.0.0-3.47100.x86_64.rpm
```
### iperf3
```
yum install -y iperf3
```
### iftop
```
yum -y install libpcap libpcap-devel ncurses ncurses-devel
yum install -y iperf3
wget http://www.ex-parrot.com/pdw/iftop/download/iftop-0.17.tar.gz
tar -zxvf iftop-0.17.tar.gz
cd iftop-0.17
./configure
make
make install
```
### hamachi
#### install
```
wget https://www.vpn.net/installers/logmein-hamachi-2.1.0.203-x64.tgz
tar xvf logmein-hamachi-2.1.0.203-x64.tgz
cd logmein-hamachi-2.1.0.203-x64
./install.sh
```
#### login
```
hamachi login
```
#### create
```
hamachi create <group id>
```
### join
```
hamachi join <group id>
```
## 各種查看指令
### 版本
#### linux核心版本
```
uname -r
```
#### linux distribution
```
cat /etc/redhat-release
```
### 磁區
#### 所有mount點
```
df -h
```
#### partition相關
```
fdisk -l
parted -l
```
#### 磁區關聯
```
lsblk
```
### 套件 (以gcc為例)
#### 已安裝
##### rpm
```
rpm -qa | grep gcc
```
##### yum
```
yum list installed | grep gcc
```
#### 未安裝
```
yum search gcc
```
#### 未安裝＋版本
```
yum --showduplicates list gcc
```
## AOCC (option)
### install
```bash
wget https://developer.amd.com/aocc-compiler-eula/aocc-compiler-2.1.0.tar
tar vxf aocc-compiler-2.1.0.tar
cd aocc-compiler-2.1.0
./install.sh
mkdir /usr/local/Modules/modulefiles/aocc
cp /root/aocc-compiler-2.1.0_module /usr/local/Modules/modulefiles/aocc/2.1.0
```
## flame (option)
```bash
git clone https://github.com/amd/libflame.git
cd libflame
./configure --enable-dynamic-build --enable-builtin-blas \
--enable-lapack2flame --enable-supermatrix \
--enable-multithreading=openmp --enable-gpu \
--enable-cblas-interfaces --prefix=/usr/local/libflame
make -j16
make install
```
## 把系統維持在舊版本的方法 (CentOS 6.9)
```bash
yum-config-manager --disable CentOS\*
```
```bash
vi /etc/yum.repos.d/CentOS-Vault.repo
```
加入以下行數到最後
```bash
[C6.9-base]
name=CentOS-6.9 - Base
baseurl=http://vault.centos.org/6.9/os/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-6
enabled=0
[C6.9-updates]
name=CentOS-6.9 - Updates
baseurl=http://vault.centos.org/6.9/updates/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-6
enabled=0
[C6.9-extras]
name=CentOS-6.9 - Extras
baseurl=http://vault.centos.org/6.9/extras/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-6
enabled=0
[C6.9-contrib]
name=CentOS-6.9 - Contrib
baseurl=http://vault.centos.org/6.9/contrib/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-6
enabled=0
[C6.9-centosplus]
name=CentOS-6.9 - CentOSPlus
baseurl=http://vault.centos.org/6.9/centosplus/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-6
enabled=0
```
```bash
yum-config-manager --enable C6.9\*
```
## 手動分磁區 (限 LVM)
### 把 home 變 50G
```bash
yum install -y gdisk
umount /dev/mapper/VolGroup-lv_home
e2fsck -f /dev/mapper/VolGroup-lv_home
resize2fs /dev/mapper/VolGroup-lv_home 50G
mount /dev/mapper/VolGroup-lv_home /home
lvreduce -L 50G /dev/mapper/VolGroup-lv_home
```
### 把 root 變 1.6T
```bash
lvextend -L 1.6T /dev/VolGroup/lv_root
resize2fs /dev/VolGroup/lv_root
```
## 手動編 environment module
### installation
```bash
cd /tmp
wget https://github.com/cea-hpc/modules/releases/download/v4.4.1/modules-4.4.1.tar.gz
tar xvf modules-4.4.1.tar.gz -C /opt
cd /opt/modules-4.4.1
./configure --prefix=/usr/share/Modules
make -j16
make install -j16
echo ". /usr/share/Modules/init/bash" > /etc/profile.d/module.sh
exec bash
```
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