[CP2K-user] [CP2K:13765] CP2K 7.1 memory leak

[Adams ke]

Hi,
     Have you solved this problem ?

On Tuesday, August 18, 2020 at 7:09:26 PM UTC+8 Paul Schwarz wrote:

> Hi Ole,
>
> Regarding toolchain:
> Yes, that was the right issue. I added the codelines from the updated 
> toolchain script to my own and compiled a pdbg binary.
>
> Regarding the memory leaks:
> I ran a geometry optimization for two different systems with the pdbg 
> binary: one that does not run out of memory before finishing, and one that 
> does run out of memory before finishing.
>
> In the first case, I got messages from the leak sanitizer in the end, and 
> I attach the output at the end of this post.
> Since I run my calculations with 'nohup ... &', I got the sanitizer 
> messages written to nohup.out.
> The leaks seem to come from
>     /usr/lib/x86_64-linux-gnu/liblsan.so
>     /opt/intel_.../linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so
>     /lib/x86_64-linux-gnu/libc.so
>
> However, I'm not familiar with debugging code, and it seems to me that 
> 1280 bytes of leaked memory in 8 objects is not much.
>
> In the second case, though, the leak sanitizer did not write anything to 
> nohup.out and the simulation just crashed as before, as it ran out of 
> memory.
> I thought that there might be some problem, since I'm running this 
> calculation via the ASE interface and maybe some information got lost, I 
> don't know.
> So I restarted the simulation, but now with the standard cp2k.pdbg, and 
> not cp2k_shell.pdbg.
> Here, I'm currently tracking the memory usage of my machine and I see that 
> the memory usage increases from ~24 GB to 35 GB over rougly 170 minutes.
>
> Even though I did not track the memory usage for the first case, I think 
> that the memory usage must have grown in the same way.
> And I don't really understand how the reported 1280 bytes of leaked memory 
> could lead to such a large increase of memory usage.
>
>
> Best regards
> Paul
>
>
> ========================================================
> Leak sanitizer output:
>
> ==42842==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7f09c65047e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7f09318f36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7f09c6503acb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7f09c34a8a29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>
> =================================================================
> ==42843==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7fe1887c47e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7fe0f3bf36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7fe1887c3acb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7fe185768a29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>
> =================================================================
> ==42844==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7f4564a917e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7f44cfef36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7f4564a90acb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7f4561a35a29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>
> =================================================================
> ==42845==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7faa81dbf7e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7fa9ed1f36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>
> =================================================================
> ==42846==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7f54b0dcb7e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7f541c1f36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7f54b0dcaacb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7f54add6fa29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>
> =================================================================
> ==42848==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7ff87ac327e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7ff7e5ff36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7ff87ac31acb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7ff877bd6a29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>     #0 0x7faa81dbeacb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7faa7ed63a29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>
> =================================================================
> ==42847==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7f1b63ff97e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7f1acf3f36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7f1b63ff8acb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7f1b60f9da29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
> =================================================================
> ==42841==ERROR: LeakSanitizer: detected memory leaks
>
> Direct leak of 1280 byte(s) in 8 object(s) allocated from:
>     #0 0x7f50707517e3  (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xf7e3)
>     #1 0x7f4fdbaf36b7 in rxm_cmap_alloc_handle 
> (/opt/devel/intel/compilers_and_libraries_2019.5.281/linux/mpi/intel64/libfabric/lib/prov/librxm-fi.so+0x86b7)
>
> Direct leak of 27 byte(s) in 5 object(s) allocated from:
>     #0 0x7f5070750acb in __interceptor_malloc 
> (/usr/lib/x86_64-linux-gnu/liblsan.so.0+0xeacb)
>     #1 0x7f506d6f5a29 in __strdup (/lib/x86_64-linux-gnu/libc.so.6+0x9da29)
>
> SUMMARY: LeakSanitizer: 1307 byte(s) leaked in 13 allocation(s).
>
>
>
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