Memory error - Githubissues

Albert-Shuai commented 2 years ago

Hi Dr. Bo Li:

I am trying to use GIANA-4.1 to perform cluster on around 3000,000 sequences, without vdj gene information. I request 128G memory, but it still gives:

Traceback (most recent call last): File "/users/sli1/GIANA-4.1/GIANA4.1.py", line 1255, in main() File "/users/sli1/GIANA-4.1/GIANA4.1.py", line 1251, in main EncodeRepertoire(ff, OutDir, OutFile, ST=ST, thr_s=thr_s, thr_v=thr_v, exact=EE,VDict=VScore, Vgene=VV, thr_iso=cutoff, gap=Gap, GPU=GPU, Mat=Mat, verbose=verbose) File "/users/sli1/GIANA-4.1/GIANA4.1.py", line 919, in EncodeRepertoire SSGnew=UpdateSSG(SSG, CDR3s, tmpVgenes, Vscore=VDict, cutoff=thr_s+4) File "/users/sli1/GIANA-4.1/GIANA4.1.py", line 548, in UpdateSSG N=len(list(chain(*list(SSG.values())))) MemoryError

In the paper you mentioned that GIANA is fast on 10^7 scale sequence clustering, thus may I learn that how many memory shall I apply for for my task. Thanks!

davidcoffey commented 4 months ago

I am also getting a "MemoryError" when trying to run GIANA4.1.py on a file with 1,744,942 sequences. My file does contain V gene names in IMGT format. I am running the job on a Linux cluster using SLURM resource manager and have allocated 512 GB of RAM and 12 CPUs. Jobs with fewer sequences run successfully. The tutorial data file also runs successfully. I have tried running it with and without non-exact mode (-e).

python GIANA4.1.py -b -e -f $FILE

Creating CDR3 list
---Process CDR3s with length 18 ---
 Performing CDR3 encoding
 The number of sequences is 1744942
 Done! Total time elapsed 95.277371
==========================================================================
type I break
     Handling identical CDR3 groups
 Done! Total time elapsed 10224.895391
     Matching variable genes
Traceback (most recent call last):
  File "GIANA4.1.py", line 1257, in <module>
    main()
  File "GIANA4.1.py", line 1253, in main
    EncodeRepertoire(ff, OutDir, OutFile, ST=ST, thr_s=thr_s, thr_v=thr_v, exact=EE,VDict=VScore, Vgene=VV, thr_iso=cutoff, gap=Gap, GPU=GPU, Mat=Mat, verbose=verbose)
  File "GIANA4.1.py", line 852, in EncodeRepertoire
    vCL=IdentifyMotifCluster(sMat)
  File "GIANA4.1.py", line 598, in IdentifyMotifCluster
    STACK=dfs(SSG,ii)
  File "GIANA4.1.py", line 581, in dfs
    stack.extend(set(graph[vertex]) - visited)
MemoryError

s175573 commented 4 months ago

Could you please make sure that you only have 17K sequences input? According to GIANA message, there are 1.7M sequences for length 18 alone.

Best, Bo

From: David Coffey, MD @.> Date: Saturday, February 10, 2024 at 9:48 PM To: s175573/GIANA @.> Cc: Subscribed @.***> Subject: Re: [s175573/GIANA] Memory error (Issue #2) EXTERNAL MAIL

I am also getting a "MemoryError" when trying to run GIANA4.1.py on a file with 17,194 sequences. My file does contain V gene names in IMGT format. I am running the job on a Linux cluster using SLURM resource manager and have allocated 512 GB of RAM and 12 CPUs. Jobs with fewer sequences run successfully. The tutorial data file also runs successfully. I have tried running it with and without non-exact mode (-e).

python GIANA4.1.py -b -e -f $FILE

Creating CDR3 list

---Process CDR3s with length 18 ---

Performing CDR3 encoding

The number of sequences is 1744942

Done! Total time elapsed 95.277371

==========================================================================

type I break

 Handling identical CDR3 groups

Done! Total time elapsed 10224.895391

 Matching variable genes

Traceback (most recent call last):

File "GIANA4.1.py", line 1257, in

main()

File "GIANA4.1.py", line 1253, in main

EncodeRepertoire(ff, OutDir, OutFile, ST=ST, thr_s=thr_s, thr_v=thr_v, exact=EE,VDict=VScore, Vgene=VV, thr_iso=cutoff, gap=Gap, GPU=GPU, Mat=Mat, verbose=verbose)

File "GIANA4.1.py", line 852, in EncodeRepertoire

vCL=IdentifyMotifCluster(sMat)

File "GIANA4.1.py", line 598, in IdentifyMotifCluster

STACK=dfs(SSG,ii)

File "GIANA4.1.py", line 581, in dfs

stack.extend(set(graph[vertex]) - visited)

MemoryError

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davidcoffey commented 4 months ago

Yes, that was a type-o. In the example above, I have 1.7M sequences, each 18 amino acids in length. Since I noticed clustering is done on equal-length CDR3 sequences, I chose to subset up my entire dataset into separate files with sequences of the same size and am running each file in parallel (I have 65M sequences in total). I did attempt to run the entire dataset through GIANA with 1.5TB of allocated memory, and after 3 weeks, there has been no progress.

s175573 / GIANA

Memory error #2