0 votes
asked by (690 points)

Hi Miles,

I recently came across a strange error when trying to save MPS to a .h5 file when running the code on multiple cores (because single core doesn't have enough memory for large bond dimension).

For small enough bond dimension, when I use a single core, everything works fine. However, when I set the number of cores to be more than 1, then I got an error, copy and pasted at the end. For creating and writing into the file, I used the standard
f = h5open("mps-$N-free.h5","w")
write(f,"mps-$N-free",psi)
close(f)

Is it because this way of creating and writing the file doesn't support multicore processes? I'm not sure if you have seen this kind of error before.
Thanks a lot for your time
-Mason

HDF5-DIAG: Error detected in HDF5 (1.12.0) thread 0:
#000: H5F.c line 705 in H5Fcreate(): unable to create file
major: File accessibility
minor: Unable to open file
#001: H5VLcallback.c line 3393 in H5VLfilecreate(): file create failed
major: Virtual Object Layer
minor: Unable to create file
#002: H5VLcallback.c line 3358 in H5VLfilecreate(): file create failed
major: Virtual Object Layer
minor: Unable to create file
#003: H5VLnative
file.c line 65 in H5VL
nativefilecreate(): unable to create file
major: File accessibility
minor: Unable to open file
#004: H5Fint.c line 1707 in H5F_open(): unable to read superblock
major: File accessibility
minor: Read failed
#005: H5Fsuper.c line 412 in H5F__super_read(): file signature not found
major: File accessibility
minor: Not an HDF5 file
ERROR: LoadError: Error creating file mps-10-free.h5
Stacktrace:
[1] error(::String, ::String)
@ Base ./error.jl:42
[2] h5f_create
@ ~/.julia/packages/HDF5/0iEnL/src/api.jl:504 [inlined]
[3] h5open(filename::String, mode::String; swmr::Bool, pv::Base.Iterators.Pairs{Union{}, Unn
ion{}, Tuple{}, NamedTuple{(), Tuple{}}})
@ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:428
[4] h5open(filename::String, mode::String)
@ HDF5 ~/.julia/packages/HDF5/0iEnL/src/HDF5.jl:412
[5] top-level scope
@ ~/new/D10/N-30-free/CFermion.jl:382
in expression starting at /public1/home/sc61251/new/D10/N-30-free/CFermion.jl:192

1 Answer

0 votes
answered ago by (690 points)

For people that are interested, I accidentally found a way around this.

The original shell script I tried for job submission contains the following:
#SBATCH -n 6
srun -n 4
where the -n 6 means saving 6 cores for the calculation, and the -n 4 means using 4 of them. The purpose of the extra 2 cores is to provide some more memory space in case the 4 cores aren't enough, so that the job wouldn't be killed.

It's exactly the -n 4 cores used that seems to be giving me the problem in creating the .h5 file and save data, which I still haven't figured out why. In my new shell script, I simply changed the -n 4 to be -n 1, which surprisingly worked very well. It's a single core, so no file creation issue, and at the same time we have the 6 cores backup, so no memory issue.

My initial misconception was that the srun -n has to take care of the most part of the memory consumption, so that in order to resolve the memory issue, it has to be more than 1 core. This turned out not to be the case. Again, I still don't know why due to my very limited knowledge in computer science.

Hopefully this could be useful to people in the future, and I would also love to hear about why this is the case from the experts.

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