Qcxms

[zargham-ahmad]

This PR includes the following: #419

• added qcxms_neutral_run tool, which outputs three collections (apart from the additional output) which are further used by qcxms_prod_run.
• added qcxms_prod_run which uses three collections from qcxms_neutral_run and outputs two files one is log file and the other is result.jdx file

TODO:

• [x] update the qcxms version to 5.2.1
• [ ] option to use pqcxms command in qcxms_prod_run (cannot use until the next release because of the prod flag issue https://github.com/qcxms/QCxMS/pull/80)
• [x] add plotms as a requirement after the package gets on conda

[hechth]

@zargham-ahmad please add a description for this PR shortly outlining the tool added and what was done for documentation purposes.

[zargham-ahmad]

@zargham-ahmad please add a description for this PR shortly outlining the tool added and what was done for documentation purposes.

done

[zargham-ahmad]

qcxms is failing for more trajectories with the following error but the compiled binary from qcxms github seems to be working fine

free(): invalid pointer

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:
#0  0x7f6eece94fcf in ???
#1  0x7f6eecee3d3c in ???
#2  0x7f6eece94f31 in ???
#3  0x7f6eece7f471 in ???
#4  0x7f6eeced833f in ???
#5  0x7f6eeceed6b9 in ???
#6  0x7f6eeceef443 in ???
#7  0x7f6eecef1d9e in ???
#8  0x560b5c56e05e in ???
#9  0x560b5c535ef5 in ???
#10  0x560b5c533060 in ???
#11  0x7f6eece801c9 in ???
#12  0x7f6eece80284 in ???
#13  0x560b5c533090 in ???

[zargham-ahmad]

Hi, the conda forge version of the qcxms is failing with the below error. @bgruening @JayTheDog, do you have any idea?

free(): invalid pointer

Program received signal SIGABRT, Aborted. __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50 50 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory. (gdb) bt

0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50

1 0x00007ffff56fe859 in __GI_abort () at abort.c:79

2 0x00007ffff576926e in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff5893298 "%s\n")

at ../sysdeps/posix/libc_fatal.c:155

3 0x00007ffff57712fc in malloc_printerr (str=str@entry=0x7ffff58914c1 "free(): invalid pointer") at malloc.c:5347

4 0x00007ffff5772b2c in _int_free (av=, p=, have_lock=0) at malloc.c:4173

5 0x000055555559305f in __qcxms_write_fragments_MOD_manage_fragments ()

6 0x000055555555aef6 in MAIN__ ()

(gdb) continue Continuing.

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

0 0x7ffff571f08f in ???

    at /build/glibc-BHL3KM/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0

1 0x7ffff571f00b in __GI_raise

    at ../sysdeps/unix/sysv/linux/raise.c:51

2 0x7ffff56fe858 in __GI_abort

    at /build/glibc-BHL3KM/glibc-2.31/stdlib/abort.c:79

3 0x7ffff576926d in __libc_message

    at ../sysdeps/posix/libc_fatal.c:155

4 0x7ffff57712fb in malloc_printerr

    at /build/glibc-BHL3KM/glibc-2.31/malloc/malloc.c:5347

5 0x7ffff5772b2b in _int_free

    at /build/glibc-BHL3KM/glibc-2.31/malloc/malloc.c:4173

6 0x55555559305e in ???

7 0x55555555aef5 in ???

8 0x555555558060 in ???

9 0x7ffff5700082 in __libc_start_main

    at ../csu/libc-start.c:308

10 0x555555558090 in ???

Program received signal SIGABRT, Aborted. __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50

[JayTheDog]

Hi, the conda forge version of the qcxms is failing with the below error. @bgruening @JayTheDog, do you have any idea?

free(): invalid pointer

Program received signal SIGABRT, Aborted. GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50 50 ../sysdeps/unix/sysv/linux/raise.c: No such file or directory. (gdb) bt #0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50 #1 0x00007ffff56fe859 in GI_abort () at abort.c:79 #2 0x00007ffff576926e in __libc_message (action=action@entry=do_abort, fmt=fmt@entry=0x7ffff5893298 "%s\n") at ../sysdeps/posix/libc_fatal.c:155 #3 0x00007ffff57712fc in malloc_printerr (str=str@entry=0x7ffff58914c1 "free(): invalid pointer") at malloc.c:5347 #4 0x00007ffff5772b2c in _int_free (av=, p=, have_lock=0) at malloc.c:4173 #5 0x000055555559305f in qcxms_write_fragments_MOD_manage_fragments () #6 0x000055555555aef6 in MAIN () (gdb) continue Continuing.

Program received signal SIGABRT: Process abort signal.

Backtrace for this error: #0 0x7ffff571f08f in ??? at /build/glibc-BHL3KM/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0 #1 0x7ffff571f00b in GI_raise at ../sysdeps/unix/sysv/linux/raise.c:51 #2 0x7ffff56fe858 in __GI_abort at /build/glibc-BHL3KM/glibc-2.31/stdlib/abort.c:79 #3 0x7ffff576926d in libc_message at ../sysdeps/posix/libc_fatal.c:155 #4 0x7ffff57712fb in malloc_printerr at /build/glibc-BHL3KM/glibc-2.31/malloc/malloc.c:5347 #5 0x7ffff5772b2b in _int_free at /build/glibc-BHL3KM/glibc-2.31/malloc/malloc.c:4173 #6 0x55555559305e in ??? #7 0x55555555aef5 in ??? #8 0x555555558060 in ??? #9 0x7ffff5700082 in __libc_start_main at ../csu/libc-start.c:308 #10 0x555555558090 in ???

Program received signal SIGABRT, Aborted. __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50

At what point does this happen? I currently don't have the capability to check whether this problem occurs only for some trajectories, or for the entirety of the runs. @gorges has the capabilities for this, we should make him part of this conversation

[hechth]

@zargham-ahmad you mentioned that it works with a single trajectory but not multiple, is that right?

[hechth]

@JayTheDog @bgruening @gorges97 I think it is related to the compilation for conda-forge. I ran now 3 trajectories locally and the tool peaked at 61GB memory consumption using the binary from conda forge - probably some optimizations are not available or the compiler flags are not passed correctly?

Or do you think the difference comes from the absence of the intel mkl and blas libraries?

[bgruening]

https://github.com/conda-forge/qcxms-feedstock/blob/main/recipe/build.sh

What is missing here?