When I was compiling CMAKE-3.11.4 with GNU-5.4.0, we encountered the error
"The C++ compiler does not support C++11 (e.g. std::unique_ptr)"
This was rather complex to solve. I believe if I upgrade my GNU Compilers, it might work. Somehow at GNU 5.4, it does not recognize the C++11 support.
But when I downgraded to Cmake-3.9.6, it works immediately without issues. Do look at https://cmake.org/files/v3.9/
# cd $CMAKE_HOME #./bootstrap # gmake
“Crucially, because the BMC has the ability to install the operating system, it can disrupt the process that boots the operating system – and fetch potentially malicious implant code, maybe even over the Internet.”
An Interesting Read “Making sense of the Supermicro motherboard attack” from Light Blue Touchpaper
Here is a write-up of my computing platform and applications:
Step 1: First thing first, source the intel components setting from
source /usr/local/intel/2018u3/bin/compilervars.sh intel64 source /usr/local/intel/2018u3/impi/2018.3.222/bin64/mpivars.sh intel64 source /usr/local/intel/2018u3/mkl/bin/mklvars.sh intel64 source /usr/local/intel/2018u3/parallel_studio_xe_2018/bin/psxevars.sh intel64
export NWCHEM_TOP=/usr/local/software/nwchem-6.8/nwchem-6.8
export NWCHEM_MODULES=pnnl
export NWCHEM_TARGET=LINUX64
export NWCHEM_LONG_PATHS=y
export PYTHONHOME=/usr
export PYTHONVERSION=2.7
export PYTHONLIBTYPE=so
export USE_PYTHON64=y
export USE_NOFSCHECK=y
export TCGRSH=/usr/bin/ssh
export LARGE_FILES=y
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC="/usr/local/intel/2018u3/impi/2018.3.222/intel64"
export MPI_INCLUDE="/usr/local/intel/2018u3/impi/2018.3.222/intel64/include/gfortran/5.1.0 -I/usr/local/intel/2018u3/impi/2018.3.222/intel64/include"
export MPI_LIB="/usr/local/intel/2018u3/impi/2018.3.222/intel64/lib/release_mt -L/usr/local/intel/2018u3/impi/2018.3.222/intel64/lib"
export LIBMPI="-lmpifort -lmpi -lmpigi -ldl -lrt -lpthread"
export USE_OPENMP=y
export MKLROOT=/usr/local/intel/2018u3/mkl
export MKLLIB="${MKLROOT}/lib/intel64"
export MKLINC="${MKLROOT}/include"
export HAS_BLAS=y
export BLAS_SIZE=8
export BLASOPT="-L${MKLROOT}/lib/intel64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -liomp5 -lpthread -lm -ldl"
export LAPACK_SIZE=8
export LAPACK_LIB="$BLASOPT"
export LAPACK_LIBS="$BLASOPT"
export LAPACKOPT="$BLASOPT"
export USE_SCALAPACK=y
export SCALAPACK_SIZE=8
export SCALAPACK="-L${MKLROOT}/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_intel_thread -lmkl_core -lmkl_blacs_intelmpi_ilp64 -liomp5 -lpthread -lm -ldl"
export SCALAPACK_LIB="$SCALAPACK"
export SCALAPACK_LIBS="$SCALAPACK"
export CC=icc
export FC=ifort
export USE_64TO32=y
cd $NWCHEM_TOP/src
#make realclean
make nwchem_config
make 64_to_32
make CC=icc FC=ifort FOPTIMIZE=-O3
cd $NWCHEM_TOP/src/tools
make CC=icc FC=ifort FOPTIMIZE=-O3 version
make CC=icc FC=ifort FOPTIMIZE=-O3
cd $NWCHEM_TOP/src
make CC=icc FC=ifort FOPTIMIZE=-O3 link
General Site Installation
Determine the local storage path for the install files. (e.g., /usr/local/NWChem).
Make directories
Determine the local storage path for the install files. (e.g., /usr/local/NWChem).
Make directories
# mkdir /usr/local/nwchem-6.8 # mkdir /usr/local/nwchem-6.8/bin # mkdir /usr/local/nwchem-6.8/data
Copy binary
# cp $NWCHEM_TOP/bin/ /usr/local/nwchem-6.8/bin # cd /usr/local/nwchem-6.8/bin # chmod 755 nwchem
Copy libraries
# cd $NWCHEM_TOP/src/basis # cp -r libraries /usr/local/nwchem-6.8/data # cd $NWCHEM_TOP/src/ # cp -r data /usr/local/nwchem-6.8 # cd $NWCHEM_TOP/src/nwpw # cp -r libraryps /usr/local/nwchem-6.8/data
The Final Lap (From Compiling NWChem)
Each user will need a .nwchemrc file to point to these default data files. A global one could be put in /usr/local/nwchem-6.8/data and a symbolic link made in each users $HOME directory is probably the best plan for new installs. Users would have to issue the following command prior to using NWChem: ln -s /usr/local/nwchem-6.8/data/default.nwchemrc $HOME/.nwchemrc
Contents of the default.nwchemrc file based on the above information should be:
nwchem_basis_library /usr/local/nwchem-6.8/data/libraries/ nwchem_nwpw_library /usr/local/nwchem-6.8/data/libraryps/ ffield amber amber_1 /usr/local/nwchem-6.8/data/amber_s/ amber_2 /usr/local/nwchem-6.8/data/amber_q/ amber_3 /usr/local/nwchem-6.8/data/amber_x/ amber_4 /usr/local/nwchem-6.8/data/amber_u/ spce /usr/local/nwchem-6.8/data/solvents/spce.rst charmm_s /usr/local/nwchem-6.8/data/charmm_s/ charmm_x /usr/local/nwchem-6.8/data/charmm_x/
References:
Step 1: Copy /etc/pbs.conf from any of the existing node to /etc of the new node
# scp -v /etc/pbs.conf root@remotenode:/etc
Step 2: Install Pbs execution rpm on the new node
# rpm -Uvh /usr/local/software/admin/altair/PBSPro_14.2.5/pbspro-execution-14.2.5.20180221140231-0.el7.x86_64.rpm
Step 3: Copy /var/spool/pbs/mom_priv/config from any existing node to /var/spool/pbs/mom_priv of new node
# scp -v /var/spool/pbs/mom_priv/config root@remotenode:/var/spool/pbs/mom_priv/
Step 4. “service pbs restart “ on the new node
# service pbs restart
Step 5. Create the node on PBS-Server
# qmgr -c “create node node-name"
If you are implementing PBS-Pro Display Manager, you have to open ports TCp/UDP 5901-5920
Note: Do note that the default zone is “public”
Section 1: Checking Zones and Prerequisites
Option 1: Check State of Firewalld
# firewall-cmd --state Running
Option 2: Check Default Zone
# firewall-cmd --get-default-zone public
Option 3: Check Active Zones
# firewall-cmd --get-active-zones public: etho eth1
Option 4: Get Zones
# firewall-cmd --get-zones block dmz drop external home internal public trusted work
Section 2: Selecting Zones for your Interfaces
Option 1: Change Interfaces
# firewall-cmd --permanent --zone=trusted --change-interface=eth0 success
# firewall-cmd --reload
Option 2: Verify the Zone has been changed
firewall-cmd --get-active-zones
trusted interfaces: eth0 public interfaces: eth1
Section 3: Editing Firewall-CMD Rules
Option 1: Opening Ports (Single)
# firewall-cmd --permanent --zone=public --add-port=80/tcp success # firewall-cmd --reload
Option 2: Opening Ports (Range)
# firewall-cmd --permanent --zone=public --add-port=80-90/tcp success # firewall-cmd --reload
Option 3: List Ports
# firewall-cmd --zone=public --list-all public (active) target: default icmp-block-inversion: no interfaces: enp6s0f0 eno2 ib1 sources: services: ssh dhcpv6-client ports: 22/tcp 5053/tcp 57889/tcp protocols: masquerade: no forward-ports: source-ports: icmp-blocks: rich rules:
Option 4: Remove Port
# firewall-cmd --permanent --zone=public --remove-port=80/tcp success # firewall-cmd --reload
Option 5: Adding Service
Checking Services
# firewall-cmd --get-services
RH-Satellite-6 amanda-client amanda-k5-client bacula bacula-client bitcoin bitcoin-rpc bitcoin-testnet bitcoin-testnet-rpc ceph ceph-mon cfengine condor-collector ctdb dhcp dhcpv6 dhcpv6-client dns docker-registry dropbox-lansync elasticsearch freeipa-ldap freeipa-ldaps freeipa-replication freeipa-trust ftp ganglia-client ganglia-master high-availability http https imap imaps ipp ipp-client ipsec iscsi-target kadmin kerberos kibana klogin kpasswd kshell ldap ldaps libvirt libvirt-tls managesieve mdns mosh mountd ms-wbt mssql mysql nfs nfs3 nrpe ntp openvpn ovirt-imageio ovirt-storageconsole ovirt-vmconsole pmcd pmproxy pmwebapi pmwebapis pop3 pop3s postgresql privoxy proxy-dhcp ptp pulseaudio puppetmaster quassel radius rpc-bind rsh rsyncd samba samba-client sane sip sips smtp smtp-submission smtps snmp snmptrap spideroak-lansync squid ssh synergy syslog syslog-tls telnet tftp tftp-client tinc tor-socks transmission-client vdsm vnc-server wbem-https xmpp-bosh xmpp-client xmpp-local xmpp-server
Finally, Add Service
# firewall-cmd --permanent --zone=public --add-service=http success # firewall-cmd --reload
References:
Step 1: Check current kernel version
# uname -r 3.10.0-862.14.4.el7.x86_64
Step 2: Check installed kernel version
# yum info kernel Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.0x.sg * elrepo: elrepo.mirror.angkasa.id * epel: sg.fedora.ipserverone.com * extras: mirror.0x.sg * updates: mirror.0x.sg Installed Packages Name : kernel Arch : x86_64 Version : 3.10.0 Release : 693.el7 Size : 59 M Repo : installed From repo : anaconda Summary : The Linux kernel URL : http://www.kernel.org/ License : GPLv2 Description : The kernel package contains the Linux kernel (vmlinuz), the core of any : Linux operating system. The kernel handles the basic functions : of the operating system: memory allocation, process allocation, device : input and output, etc. Name : kernel Arch : x86_64 Version : 3.10.0 Release : 862.14.4.el7 Size : 62 M Repo : installed From repo : updates Summary : The Linux kernel URL : http://www.kernel.org/ License : GPLv2 Description : The kernel package contains the Linux kernel (vmlinuz), the core of any : Linux operating system. The kernel handles the basic functions : of the operating system: memory allocation, process allocation, device : input and output, etc.
Step 3: Install Kernel-Devel and Kernel-Headers
# yum install kernel-devel kernel-headers -y
# yum info kernel-devel kernel-headers
Step 4: Check Kernel-Devel. Make sure the version is in-sync
# yum info kernel-devel Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.0x.sg * elrepo: elrepo.mirror.angkasa.id * epel: sg.fedora.ipserverone.com * extras: mirror.0x.sg * updates: mirror.0x.sg Installed Packages Name : kernel-devel Arch : x86_64 Version : 3.10.0 Release : 862.14.4.el7 Size : 37 M Repo : installed From repo : updates Summary : Development package for building kernel modules to match the kernel URL : http://www.kernel.org/ License : GPLv2 Description : This package provides kernel headers and makefiles sufficient to build modules : against the kernel package.
Step 5: Check Kernel-Headers. Make sure the version is in-sync
# yum info kernel-headers Loaded plugins: fastestmirror, langpacks Loading mirror speeds from cached hostfile * base: mirror.0x.sg * elrepo: elrepo.mirror.angkasa.id * epel: sg.fedora.ipserverone.com * extras: mirror.0x.sg * updates: mirror.0x.sg Installed Packages Name : kernel-headers Arch : x86_64 Version : 3.10.0 Release : 862.14.4.el7 Size : 3.6 M Repo : installed From repo : updates Summary : Header files for the Linux kernel for use by glibc URL : http://www.kernel.org/ License : GPLv2 Description : Kernel-headers includes the C header files that specify the interface : between the Linux kernel and userspace libraries and programs. The : header files define structures and constants that are needed for : building most standard programs and are also needed for rebuilding the : glibc package.
Prerequistics:
SERVER ABAQUS_LIC_SVR 000000000 27000 VENDOR ABAQUSLM port=27398 ..... ..... .....
Step 1: Shutting down the License Server
# cd /usr/SIMULIA/License/2017/linux_a64/code/bin/ # lmdown # lmstat -a
Step 2: Starting the License Server
# lmgrd -c ABAQUS_LIC_SVR.LIC -l 081018.log
