What is RELION?
RELION (REgularized LIkelihood OptimizatioN) is an open-source program for the refinement of macromolecular structures by single-particle analysis of electron cryomicroscopy (cryo-EM) data
RELION (REgularized LIkelihood OptimizatioN) implements an empirical Bayesian approach for analysis of electron cryo-microscopy (Cryo-EM)
RELION provides refinement methods of singular or multiple 3D reconstructions as well as 2D class averages
RELION is an important tool in the study of living cellsHPC-AI Advisory Council
Performance Analysis Summary
(from Article See RELION – Performance Benchmark and Profiling)
RELION performance testing
- Pool size 4,8,16 gave best performance on 16,24,32 nodes
- SHARP In-Network Computing reduces MPI time by 13% and increase overall application performance by 5
- Performance advantages increases with system size, up to 32 nodes were tested
- Rank #0 does not perform computation
- Mostly MPI_Barrier (70%)
- Ring communication matrix
FIO is a tool for measuring IO performance. You can use FIO to run a user-defined workload and collect the associated performance data.
A good writeup can be found at Fio Basics. For more information, do MAN on fio
Step 1: To Install fio, make sure you activated the epel repository.
# yum install fio
Parameters to be used.
% fio --filename=myfio --size=5GB --direct=1 --rw=randrw --bs=4k --ioengine=libaio --iodepth=256 --runtime=120 --numjobs=4 --time_based --group_reporting --name=iops-test-job --eta-newline=1
An entire block size or filename can be specified. For example if you are testing block size filename=/dev/sda:/dev/sdb
Indicate the size of the test file generated. If you are testing the block size and did not specify the size, the entire block will be used.
This means that the page cache is bypassed. No memory is used.
Check whether IO is access sequentially or randonly. There are a few options.
read – Sequential reading
write – Sequential Write
randread – random reading
randwrite – random writing
readwrite , rw – Mixed, sequential workload
randrw – Mixed Random Workload
Block Size. By default 4kB is used.
libaio enables asynchronous access from the application level. The option would requires –direct=1
Refers to how many requests.
Specifies the number of processes that start the jobs in parallel
Terminate processing after the specified period of time
Name of the job
fio will run for the duration of the runtime specified
Display statistics for groups of jobs as a whole instead of for each individual job. This is especially true if
numjobs is used;
Step 1: Turn off swap
Turn off swap to prevent accidental swapping. Do not that disabling swap without sufficient memory can have undesired effects
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
- Tuning Guard for AMD EPYC (pdf)
In this blog, I will write on how to turn off KSM and ksmtuned since I do not need these services and save some unnecessary swapping activities on the disk.
What is KSM?
According to RedHat Site (8.4. KERNEL SAME-PAGE MERGING (KSM)),
Kernel same-page Merging (KSM), used by the KVM hypervisor, allows KVM guests to share identical memory pages. These shared pages are usually common libraries or other identical, high-use data. KSM allows for greater guest density of identical or similar guest operating systems by avoiding memory duplication……
KSM is a Linux feature which uses this concept in reverse. KSM enables the kernel to examine two or more already running programs and compare their memory. If any memory regions or pages are identical, KSM reduces multiple identical memory pages to a single page……
8.4.4 Kernel same-page merging (KSM) has a performance overhead which may be too large for certain environments or host systems. KSM may also introduce side channels that could be potentially used to leak information across guests. If this is a concern, KSM can be disabled on per-guest basis.
# systemctl stop ksmtuned
Stopping ksmtuned: [ OK ]
# systemctl stop ksm
Stopping ksm: [ OK ]
To permanently deactivate KSM with the systemctl commands
# systemctl disable ksm
# systemctl disable ksmtuned
When KSM is disabled, any memory pages that were shared prior to deactivating KSM are still shared. To delete all of the PageKSM in the system, use the following command:
# echo 2 >/sys/kernel/mm/ksm/run
After this is performed, the khugepaged daemon can rebuild transparent hugepages on the KVM guest physical memory. Using # echo 0 >/sys/kernel/mm/ksm/run stops KSM, but does not unshare all the previously created KSM pages (this is the same as the # systemctl stop ksmtuned command).
- Redhat – 8.4. Kernel Same-Page Merging (KSM)