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.gz
Step 2: Make Standard Packages
% make yes-standard % make no-gpu % make no-mscg
Step 3: Compile message libraries
% cd lammps-15Jun20/lib/message/cslib/src % make lib_parallel zmq=no
Copy and rename the produced cslib/src/libcsmpi.a or libscnompi.a file to cslib/src/libmessage.a
% cp cslib/src/libcsmpi.a to cslib/src/libmessage.a
Copy either lammps-15Jun20/lib/message/Makefile.lammps.zmq or Makefile.lammps.nozmq to lib/message/Makefile.lammps
% cp Makefile.lammps.nozmq to Makefile.lammps
Step 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/LATTE
Inside 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.lammps
Step 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 % make
Step 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-X.Y.Z
% make -j2
% 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_002
Step 8: Finally Compile LAMMPS
% cd lammps-15Jun20/src % make g++_openmpi -j 16
You should have binary called lmp_g++_openmpi
Do a softlink
ln -s lmp_g++_openmpi lammps
Yum 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
Installing and using Mellanox HPC-X Software Toolkit
Overview
Taken from Mellanox HPC-X Software Toolkit User Manual 2.3
Mellanox HPC-X is a comprehensive software package that includes MPI and SHMEM communication libraries. HPC-X includes various acceleration packages to improve both the performance and scalability of applications running on top of these libraries, including UCX (Unified Communication X) and MXM (Mellanox Messaging), which accelerate the underlying send/receive (or put/get) messages. It also includes FCA (Fabric Collectives Accelerations), which accelerates the underlying collective operations used by the MPI/PGAS languages.
Download
https://www.mellanox.com/products/hpc-x-toolkit
Installation
% tar -xvf hpcx-v2.6.0-gcc-MLNX_OFED_LINUX-5.0-1.0.0.0-redhat7.6-x86_64.tbz
% cd hpcx-v2.6.0-gcc-MLNX_OFED_LINUX-5.0-1.0.0.0-redhat7.6-x86_64
% export HPCX_HOME=/usr/local/hpcx-v2.6.0-gcc-MLNX_OFED_LINUX-5.0-1.0.0.0-redhat7.6-x86_64
Loading HPC-X Environment from BASH
HPC-X includes Open MPI v4.0.x. Each Open MPI version has its own module file which can be used to load the desired version
% source $HPCX_HOME/hpcx-init.sh % hpcx_load % env | grep HPCX % mpicc $HPCX_MPI_TESTS_DIR/examples/hello_c.c -o $HPCX_MPI_TESTS_DIR/examples/hello_c % mpirun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_c % oshcc $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c.c -o $HPCX_MPI_TESTS_DIR/examples/ % hello_oshmem_c % oshrun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c % hpcx_unload
Loading HPC-X Environment from Modules
You can use the already built module files in hpcx.
% module use $HPCX_HOME/modulefiles % module load hpcx % mpicc $HPCX_MPI_TESTS_DIR/examples/hello_c.c -o $HPCX_MPI_TESTS_DIR/examples/hello_c % mpirun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_c % oshcc $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c.c -o $HPCX_MPI_TESTS_DIR/examples/ hello_oshmem_c % oshrun -np 2 $HPCX_MPI_TESTS_DIR/examples/hello_oshmem_c % module unload hpcx
Building HPC-X with the Intel Compiler Suite
Do take a look at the Mellanox HPC-X® ScalableHPC Software Toolkit
References:
Lenovo new 4-Socket Servers SR860-V2 and SR850-V2
This month, Lenovo launched 2 new mission-critical servers based on new 4-socket-capable third-generation Intel Xeon Scalable processors.
- ThinkSystem SR860 V2, the new 4U 4-socket server, supporting up to 48x 2.5-inch drive bays and up to 8x NVIDIA T4 GPUs or 4x NVIDIA V100S GPUs.
- ThinkSystem SR850 V2, the new 2U 4-socket server, supported up to 24x 2.5-inch drive bays, all of which can be NVMe if desired.
References:
General Linux OS Tuning for AMD EPYC
Step 1: Turn off swap
Turn off swap to prevent accidental swapping. Do not that disabling swap without sufficient memory can have undesired effects
swapoff -a
Step 2: Turn off NUMA balancing
NUMA balancing can have undesired effects and since it is possible to bind the ranks and memory in HPC, this setting is not needed
echo 0 > /proc/sys/kernel/numa_balancing
Step 3: Disable ASLR (Address Space Layout Ranomization) is a security feature used to prevent the exploitation of memory vulnerabilities
echo 0 > /proc/sys/kernel/randomize_va_space
Step 4: Set CPU governor to performance and disable cc6. Setting the CPU perfomance to governor to perfomrnaces ensures max performances at all times. Disabling cc6 ensures that deeper CPU sleep states are not entered.
cpupower frequency-set -g performance
Setting cpu: 0 Setting cpu: 1 ..... .....
cpupower idle-set -d 2
Idlestate 2 disabled on CPU 0 Idlestate 2 disabled on CPU 1 Idlestate 2 disabled on CPU 2 ..... .....
References:
Getting Useful Information on CPU and Configuration
Point 1. lscpu
To install
yum install util-linux
lscpu – (Print out information about CPU and its configuration)
[user1@myheadnode1 ~]$ lscpu Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 32 On-line CPU(s) list: 0-31 Thread(s) per core: 2 Core(s) per socket: 8 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz Stepping: 4 CPU MHz: 3200.000 BogoMIPS: 6400.00 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 25344K NUMA node0 CPU(s): 0-7,16-23 NUMA node1 CPU(s): 8-15,24-31 Flags: fpu .................
Point 2: hwloc-ls
To install hwloc-ls
yum install hwloc
hwloc – (Prints out useful information about the NUMA locality of devices and general hardware locality information)
[user1@myheadnode1 ~]# hwloc-ls Machine (544GB total) NUMANode L#0 (P#0 256GB) Package L#0 + L3 L#0 (25MB) L2 L#0 (1024KB) + L1d L#0 (32KB) + L1i L#0 (32KB) + Core L#0 PU L#0 (P#0) PU L#1 (P#16) L2 L#1 (1024KB) + L1d L#1 (32KB) + L1i L#1 (32KB) + Core L#1 PU L#2 (P#1) PU L#3 (P#17) L2 L#2 (1024KB) + L1d L#2 (32KB) + L1i L#2 (32KB) + Core L#2 PU L#4 (P#2) PU L#5 (P#18) L2 L#3 (1024KB) + L1d L#3 (32KB) + L1i L#3 (32KB) + Core L#3 PU L#6 (P#3) PU L#7 (P#19) L2 L#4 (1024KB) + L1d L#4 (32KB) + L1i L#4 (32KB) + Core L#4 PU L#8 (P#4) PU L#9 (P#20) L2 L#5 (1024KB) + L1d L#5 (32KB) + L1i L#5 (32KB) + Core L#5 PU L#10 (P#5) PU L#11 (P#21) L2 L#6 (1024KB) + L1d L#6 (32KB) + L1i L#6 (32KB) + Core L#6 PU L#12 (P#6) PU L#13 (P#22) L2 L#7 (1024KB) + L1d L#7 (32KB) + L1i L#7 (32KB) + Core L#7 PU L#14 (P#7) PU L#15 (P#23) ..... ..... .....
Point 3 – Check whether the Boost is on for AMD
Print out if CPU boost is on or off
cat /sys/devices/system/cpu/cpufreq/boost 1
References:
BOIS settings for OEM Server with EPYC
Taken from Chapter 4 of https://developer.amd.com/wp-content/resources/56827-1-0.pdf
Selected Explanation of Setting. (See Document for FULL explanation)
1. Simultaneous Mult-Threading (SMT) or HyperThreading (HT)
- IN HPC Workload, the SMT are usually turned off
2. x2APIC
- This option helps the operating system deal with interrupt more efficiently in high cores count configuration. It is recommended to enable this option. This option must be enabled if using more than 255 threads
3. Numa Per Socket (NPS)
- In many HPC applications, ranks and memory can be pinned to cores and NUMA Nodes. The recommended value should be NPS4 option. However, if the workload is not NUMA aware or suffers when the NUMA complexity increase, we can experiment with NSP1.
4. Memory Frequency, Infinity Fabric Frequency, and coupled ve uncoupled mode
Memory Clock and Infinity Fabric Clock can run at synchronous frequencies (coupled mode) or at asynchronous frequencies (uncoupled mode)
- If the memory is clocked at lower than 2933 MT/s, the memory and fabric will run in coupled mode which has the lowest memory latency
- If the memory is clocked at 3200 MT/s, the memory and fabric clock will run in asynchronous mode has higher bandwidth but increased memory latency.
- Make sure APBDIS is set to 1 and fixed SOC Pstate is set to P0
5. Preferred IO
Preferred IO allows one PCIe device in the system to be configured in a preferred mode. This device gets preferential treant on the infinity fabric
6. Determinism Slider
- Recommended to choose Power Option. For this mode, the CPUs in the system performance at the maximum capability of each silicon device. Due to the natural variation existing during the manufacturing process, some CPUs performances may be varied, but will never fall below “Performance Determinism mode”
Compiling zlib-1.2.11 with GNU 6
A Massively Spiffy Yet Delicately Unobtrusive Compression Library
Prerequisites
GNU 6.5
Compiling
wget http://www.zlib.net/zlib-1.2.11.tar.gz tar -xvzf zlib-1.2.11.tar.gz cd zlib-1.2.11 ./configure --prefix=/usr/local/zlib-1.2.11-gcc6 make check
Test Failed… does not support .pth files
If you are doing a setup.py with specific directories
python setup.py install --prefix=/home/user1
If you are getting a PythonPath Error something like this.
TEST FAILED: /home/user1/lib/python3.7/site-packages/ does NOT support .pth files error: bad install directory or PYTHONPATH You are attempting to install a package to a directory that is not on PYTHONPATH and which Python does not read ".pth" files from. The installation directory you specified (via --install-dir, --prefix, or the distutils default setting) was: /home/user1/lib/python3.7/site-packages/ and your PYTHONPATH environment variable currently contains:
You can solve like by putting in your .bashrc.
export PYTHONPATH="${PYTHONPATH}:/home/user1/lib/python3.7/site-packages/"
source ~/.bashrc
