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Hi,
I am running one of the first public releases (QCxMS.v5.0.2.tar.xz).
(1) I tested QCxMS.v5.0.2 on a newly setup VM Ubuntu 18, just fresh install.
(2) I additionally tested QCxMS.v5.0.2 on a production machine with XTB, QCEIMS, orca, TurboMole, MNDO99 etc,
basically a machine that has had no prior issues, intel compilers and intel MKL installed.
The two initial qcxms runs run fine, I get the trjM and xtb.last files as well as the individual TMP directories.
But on both machines i get the following error when executing pqcxms when running the THF CID example.
While the qcxms runs show CPU use, the pqcxms just shows 2% CPU use across all cores and doesn't even finish.
Thanks.
Tobias
~/QCxMS.v5.0/EXAMPLE/CID/Tetrahydrofuran/TMPQCXMS/TMP.1$ cat qcxms.out
Sun Jun 6 19:40:19 PDT 2021
*********************************************
* *
* Q C x M S *
* *
* V5.0.2 *
* *
* S. Grimme *
* Mulliken Center for Theoretical Chemistry *
* Universitaet Bonn *
* 2008-21 *
* Jun 1 15:00:00 CEST 2021 *
* *
*********************************************
Please cite as:
S.Grimme, Angew.Chem.Int.Ed. 52 (2013) 6306-6312.
Non-commercial. Free for academic use only.
Former Dev. : V.Asgeirsson, C.Bauer
Current Dev.: J. Koopman
xtbhome directory:/home/user/QCxMS.v5.0/.XTBPARAM/
changed by input:
>xtb2
>cid
>elab 40
>maxcoll 6
>noesi
QC method: XTB2
"Fock"-exchange ax = 0.000
************************************************************
Mode: Collision Induced Dissociation (CID)
Positive Ion mode
************************************************************
Internal program parameters (<0 means automatic):
method PosCID
prog XTB2
Dispersion D4
prog for IPs XTB2
MO spectrum XTB
ntraj 350
tstep (fs) 0.50
tmax (ps) 5.00
eimpact (eV) 40.00
CollAuto F
eTemp (K) -1.00
base eTemp (K) 5000.00
Tinit (K) 500.00
nfragexit 3
# ion tracks 7
iseed 42
----------------------------------------
qc path /usr/local/bin/
----------------------------------------
*Program selected for CID is OK*
--------------------------------------------------------------------------------
!!! M+ collisions are user set !!!
================================================================================
trajectory 1 collision 1 / 6
================================================================================
initial Cartesian coordinates:
1 13.03706 13.12782 7.35086 O 15.999
2 12.67154 10.52935 7.59640 C 12.011
3 15.07256 9.30773 8.56976 C 12.011
4 16.90149 11.49722 9.21147 C 12.011
5 15.75398 13.54767 7.27951 C 12.011
6 11.30941 10.22276 9.18509 H 1.008
7 11.85540 9.75627 5.77384 H 1.008
8 15.72251 8.29798 6.89231 H 1.008
9 14.84536 7.92434 9.99760 H 1.008
10 18.72586 10.54356 9.00469 H 1.008
11 16.80263 12.26704 11.13826 H 1.008
12 16.29815 13.31201 5.26867 H 1.008
13 16.13578 15.44135 8.06894 H 1.008
14 12.86643 14.14376 9.09913 H 1.008
statistical charge = 1.0000
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
qcxms 00000000014D9FE4 Unknown Unknown Unknown
qcxms 00000000016A41B0 Unknown Unknown Unknown
qcxms 00000000004EAFE0 areavolume_ 306 arvo.f
qcxms 00000000004EA6E3 arvo_ 95 arvo.f
qcxms 00000000004915BE mvoldrv1_ 46 mvol.f90
qcxms 0000000000426BA7 cid_ 218 cid.f90
qcxms 00000000004083AE MAIN__ 1793 main.f90
qcxms 0000000000400DEE Unknown Unknown Unknown
qcxms 00000000016A6049 Unknown Unknown Unknown
qcxms 0000000000400CCA Unknown Unknown Unknown
The text was updated successfully, but these errors were encountered:
This is a good point and might be the issue because of the xTB version implemented. The implementation of xTB will be redesigned in the near future, until then the solution provided by @zyt0y is working fine.
However, I have redesigned the way the program calculates the molecular radii because the arvo.f file was a quick fix for the issue. In the 5.0.3 release (https://github.com/qcxms/QCxMS/releases/tag/v.5.0.3), the radii are calculated by an other approach and the file is obsolete. For this reason, this issue can be regarded as fixed.
Hi,
I am running one of the first public releases (QCxMS.v5.0.2.tar.xz).
(1) I tested QCxMS.v5.0.2 on a newly setup VM Ubuntu 18, just fresh install.
(2) I additionally tested QCxMS.v5.0.2 on a production machine with XTB, QCEIMS, orca, TurboMole, MNDO99 etc,
basically a machine that has had no prior issues, intel compilers and intel MKL installed.
The two initial qcxms runs run fine, I get the trjM and xtb.last files as well as the individual TMP directories.
But on both machines i get the following error when executing pqcxms when running the THF CID example.
While the qcxms runs show CPU use, the pqcxms just shows 2% CPU use across all cores and doesn't even finish.
Thanks.
Tobias
The text was updated successfully, but these errors were encountered: