a question about parallel computing [results]

[Shiywa]

Thanks for your recent update !

I have a question about the parallel computing about pySCENIC.

Recently, I'm using the singularity to run the image "aertslab-pyscenic-0.12.0.sif". In the first step of GRN, I could control the parallel computing by set the --num_workers. However, when I set the --num_workers as 24 or other number, I found that only three or more less tasks were running.

$ top

top - 18:33:27 up  3:29,  1 user,  load average: 25.84, 26.06, 26.40
tasks: 1509 total,   3 running, 1505 sleeping,   0 stopped,   1 zombie
%Cpu(s): 19.6 us,  0.3 sy,  0.0 ni, 79.9 id,  0.0 wa,  0.0 hi,  0.2 si,  0.0 st
MiB Mem : 773867.1 total, 663837.1 free, 102458.2 used,   7571.8 buff/cache
MiB Swap:   2048.0 total,   2048.0 free,      0.0 used. 667016.0 avail Mem 

 进程号 USER      PR  NI    VIRT    RES    SHR    %CPU  %MEM     TIME+ COMMAND                               
  18932 bio       20   0 3320624   2.3g  69000 S 103.6   0.3  58:44.14 python                                
  18977 bio       20   0 3771860   2.7g  68964 S 103.6   0.4  58:38.53 python                                
  18938 bio       20   0 3742348   2.7g  69664 S 103.3   0.4  58:41.20 python                                
  18943 bio       20   0 3840500   2.8g  69652 S 103.3   0.4  58:45.79 python                                
  18959 bio       20   0 4055996   3.0g  69364 S 103.3   0.4  58:31.26 python                
...

So, I want to konw the reasons of limitation. Could please give me some advice？

My linux cluster is like

$ cat /proc/cpuinfo |grep "physical id"|sort |uniq|wc -l
2
$ cat /proc/cpuinfo |grep "processor"|wc -l
128
$ cat /proc/cpuinfo |grep "cores"|uniq
cpu cores	: 32

Could you please tell me which characteristics of machine will limit the parallel computing ?

[SeppeDeWinter]

Hi @Shiywa

Is this the case for the entire run or only specific sections?

Best,

Seppe

[Shiywa]

now, I just run GRN in my cluster. So, I don't know whether other steps will run like this.

[Shiywa]

Well, when I was running the CTX, I found that the step could run parallelly.

singularity run aertslab-pyscenic-0.12.0.sif pyscenic ctx HPV16_CC_output.tsv hg38_500bp_up_100bp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather hg38_10kbp_up_10kbp_down_full_tx_v10_clust.genes_vs_motifs.rankings.feather --annotations_fname motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl --mode dask_multiprocessing --num_workers 100 --output regulons.csv --expression_mtx_fname HPV16_CC1_count2.csv

however, I set the num_workers as 100, but the highest number of parallel tasks was 36 in my eyes. Is it normal?

[SeppeDeWinter]

I think what happened is that you happened to monitor the progress of the GRN step at a time where it did not need more than 4 cores (i.e. there were only 4 more tasks to complete so it does not make sense to use more cores in that case). That's why I asked wether it was using 4 cores for the entire time the GRN step was running. Chances are high that it was using more than 4 cores at some other time.

I can not be sure of this however.

[Shiywa]

Well, I kept monitoring the tasks in step GRN using top, but the number of the running tasks was really limited under maybe 6. By top, i could find a huge amount of tasks python with the state STOP, while only a few tasks kept running.

Actually, I want to ask which reason is the limitation of parallelly computing. I found that you mentioned "cores". My cluster has two physical cores, 32 logical cores and 128 threads. Could you please tell me which one is associated with the parameter num_workers?

Regards!

[ghuls]

num_workers is the number of threads that are spawned.