Month: July 2020
Compiling LAMMPS-15Jun20 with GNU 6 and OpenMPI 3
Prerequisites
openmpi-3.1.4
gnu-6.5
m4-1.4.18
gmp-6.1.0
mpfr-3.1.4
mpc-1.0.3
isl-0.18
gsl-2.1
lammps-15Jun20
Download the latest tar.gz from https://lammps.sandia.gov/
Step 1: Untar LAMMPS
% tar -zxvf lammps-stable.tar.gzStep 2: Go to $LAMMPS_HOME/src. Make Standard Packages
% cd src
% make yes-standard
% make no-gpu
% make no-mscgStep 3: Compile message libraries
% cd lammps-15Jun20/lib/message/cslib/src
% make lib_parallel zmq=noCopy and rename the produced cslib/src/libcsmpi.a or libscnompi.a file to cslib/src/libmessage.a
% cp cslib/src/libcsmpi.a cslib/src/libmessage.aCopy either lammps-15Jun20/lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq to lib/message/Makefile.lammps
% cp Makefile.lammps.nozmq Makefile.lammpsStep 4: Compile poems
% cd lammps-15Jun20/lib/poems
% make -f Makefile.g++Step 5: Compile latte
Download LATTE code and unpack the tarball either in this /lib/latte directory
% git clone https://github.com/lanl/LATTEInside lammps-15Jun20/lib/latte/LATTE
Modify the makefile.CHOICES according to your system architecture and compilers
% cd lammps-15Jun20/lib/latte/LATTE
% cp makefile.CHOICES makefile.CHOICES.gfort
% make% cd lammps-15Jun20/lib/latte
% ln -s ./LATTE/src includelink
% ln -s ./LATTE liblink
% ln -s ./LATTE/src/latte_c_bind.o filelink.o
% cp Makefile.lammps.gfortran Makefile.lammpsStep 6. Compile Voronoi
Download voro++-0.4.6.tar.gz from http://math.lbl.gov/voro++/download/
Untar the voro++-0.4.6.tar.gz inside lammps-15Jun20/lib/voronoi/
% tar -zxvf voro++-0.4.6.tar.gz
% cd lammps-15Jun20/lib/voronoi/voro++-0.4.6
% makeStep 7: Compile kim
Download kim from https://openkim.org/doc/usage/obtaining-models . The current version is kim-api-2.1.3.txz
Download at /lammps-15Jun20/lib/kim
% cd lammps-15Jun20/lib/kim
% tar Jxvf kim-api-2.1.3.txz% cd kim-api-2.1.3
% mkdir build
% cd build
% cmake .. -DCMAKE_INSTALL_PREFIX=${PWD}/../../installed-kim-api-2.1.3
% make -j2
% make install
% cd /lammps-15Jun20/lib/kim/installed-kim-api-2.1.3/
% source ${PWD}/kim-api-X2.1.3/bin/kim-api-activate
% kim-api-collections-management install system EAM_ErcolessiAdams_1994_Al__MO_324507536345_002Step 8: Compile USER-COLVARS
% cd lammps-15Jun/lib/colvars
% make -f Makefile.g++Step 9: Check Packages Status
% make package-status
[root@hpc-gekko1 src]# make package-status
Installed YES: package ASPHERE
Installed YES: package BODY
Installed YES: package CLASS2
Installed YES: package COLLOID
Installed YES: package COMPRESS
Installed YES: package CORESHELL
Installed YES: package DIPOLE
Installed NO: package GPU
Installed YES: package GRANULAR
Installed YES: package KIM
.....
.....Step 9a: To Activate Standard Package
% make yes-standardStep 9b: To activate USER-COLVARS, USER-OMP
% make yes-user-colvars
% make yes-user-ompStep 9c: To deactivate GPGPU
% make no-gpuStep 10: Finally Compile LAMMPS
% cd lammps-15Jun20/src
% make g++_openmpi -j 16You should have binary called lmp_g++_openmpi
Do a softlink
ln -s lmp_g++_openmpi lammpsYum History and Using Yum to Roll Back updates
Getting History of YUM actions
Point 1: List Yum actions list
(base) [root@hpc-node1 ~]# yum history list Loaded plugins: fastestmirror, langpacks ID | Login user | Date and time | Action(s) | Altered ------------------------------------------------------------------------------- 42 | root <root> | 2020-06-30 11:36 | I, U | 3 41 | 12345 | 2020-06-04 16:43 | Install | 2 40 | 12345 | 2020-06-04 16:26 | I, O, U | 878 E< 39 | 12345 | 2020-03-20 13:54 | Install | 1 > 38 | 12345 | 2020-03-20 13:46 | Install | 1 37 | 12345 | 2020-03-20 13:45 | Install | 2 36 | 12345 | 2020-03-20 13:44 | Install | 1 35 | 12345 | 2020-03-20 13:43 | Install | 28 34 | 12345 | 2020-03-20 12:52 | Update | 4 33 | 12345 | 2020-03-20 12:51 | Install | 1 32 | 12345 | 2020-03-20 12:43 | Update | 1 31 | 12345 | 2020-03-20 11:10 | Install | 1 30 | 12345 | 2020-03-20 10:53 | Install | 2 29 | 12345 | 2020-02-20 14:54 | Install | 1 28 | 12345 | 2020-01-23 16:10 | I, U | 2 27 | 12345 | 2020-01-15 15:03 | Update | 15 26 | 12345 | 2020-01-15 15:03 | I, U | 18 25 | 12345 | 2020-01-15 15:03 | Update | 3 24 | 12345 | 2019-11-07 11:00 | Install | 1 < 23 | 12345 | 2019-09-23 12:47 | Install | 1 >
Point 2: Undo the Yum action.
(base) [root@hpc-node1 boot]# yum history undo 42 Loaded plugins: fastestmirror, langpacks Undoing transaction 42, from Tue Jun 30 11:36:18 2020 ..... ..... Running transaction Installing : ntpdate-4.2.6p5-29.el7.centos.x86_64 1/4 Erasing : ntp-4.2.6p5-29.el7.centos.2.x86_64 2/4 Erasing : autogen-libopts-5.18-5.el7.x86_64 3/4 Cleanup : ntpdate-4.2.6p5-29.el7.centos.2.x86_64 4/4 Verifying : ntpdate-4.2.6p5-29.el7.centos.x86_64 1/4 Verifying : ntp-4.2.6p5-29.el7.centos.2.x86_64 2/4 Verifying : autogen-libopts-5.18-5.el7.x86_64 3/4 Verifying : ntpdate-4.2.6p5-29.el7.centos.2.x86_64 4/4 Removed: autogen-libopts.x86_64 0:5.18-5.el7 ntp.x86_64 0:4.2.6p5-29.el7.centos.2 ntpdate.x86_64 0:4.2.6p5-29.el7.centos.2 Installed: ntpdate.x86_64 0:4.2.6p5-29.el7.centos Complete!
Point 3 – Check on the history of a particular package
yum history list ntpdate
Loaded plugins: fastestmirror, langpacks
ID | Login user | Date and time | Action(s) | Altered
-------------------------------------------------------------------------------
43 | root | 2020-07-06 11:31 | D, E | 3
42 | root | 2020-06-30 11:36 | I, U | 3
40 | root | 2020-06-04 16:26 | I, O, U | 878 EE
2 | root | 2019-07-09 09:31 | I, U | 1029 EE
The Linux Cluster 