Molcas Forum

DAdrion

Member

Registered: 2022-08-04

Posts: 4

Error in restart NAMD calculations using dyn file

Hello,

I am trying to restart some dynamics NAMD calculations that crashed due to some server maintenance that we had by using the $PROJECT.dyn.h5 file provided by the dynamics calculation. When I resubmit however, I am running into an issue and the error message is not very clear (the end of the .log just says that there is "internal inconsistency in the code"). The job seems to be running smoothly up through the &dynamix keyword before it crashes right after reading the .dyn file. I have attached my input file below, along with the .err file that is provided when the calculation terminates.

&GATEWAY
 coord=$MOLCAS_PROJECT.xyz
 basis
 ano-s-mb,C_.ano-s-vdzp,O_.ano-s-vdzp,H_.ano-s-vdzp
 Group=c1
 RICD

>> FOREACH ITER in (1 .. 2)

&SEWARD
doanalytic

&RASSCF
 fileorb=$MOLCAS_PROJECT.StrOrb
 Spin=1
 Nactel=10 0 0
 Charge=0
 Ras1=0
 Ras2=9
 Ras3=0
 ITERATIONS=200,100
 CIRoot=4 4 1
 MDRLXR=2

&Surfacehop
 tully
 decoherence = 0.1

&ALASKA

&Dynamix
 velver
 dt = 20
 velo = 3
 ther= 2
 temp = 300
 H5restart=$MOLCAS_PROJECT.dyn.h5
>> End do

The error file is as follows

[ process      0]: xquit (rc =     65): _INVOKED_OTHER_MODULE_
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: ../../src/H5F.c line 1585 in H5Fopen(): unable to open file
    major: File accessibilty
    minor: Unable to open file
  #001: ../../src/H5F.c line 1403 in H5F_open(): file close degree doesn't match
    major: File accessibilty
    minor: Unable to initialize object
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: ../../src/H5A.c line 551 in H5Aopen(): not a location
    major: Invalid arguments to routine
    minor: Inappropriate type
  #001: ../../src/H5Gloc.c line 253 in H5G_loc(): invalid object ID
    major: Invalid arguments to routine
    minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: ../../src/H5A.c line 1084 in H5Aread(): not an attribute
    major: Invalid arguments to routine
    minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.12) thread 0:
  #000: ../../src/H5A.c line 2286 in H5Aclose(): not an attribute
    major: Invalid arguments to routine
    minor: Inappropriate type
[ process      0]: xquit (rc =    128): _INTERNAL_ERROR_

Program aborted. Backtrace:
#0  0x2B56FD7266D7
#1  0x2B56FD727EB2
#2  0x2B56FD7FC558
#3  0x45643A in xabort_
#4  0x447D65 in xquit_
#5  0x444588 in abend_
#6  0x42EC38 in mh5_fetch_attr_scalar_int_
#7  0x43D335 in restart_dynamix_
#8  0x406724 in dynamix_

I am not sure if there are other checkpoint files that I need to read in from the original calculation, according to the manual it just seems like I need the dyn file. I am happy to answer any questions or provide more info if need be. Thanks!

Ignacio

Administrator

From: Uppsala

Registered: 2015-11-03

Posts: 1,085

Re: Error in restart NAMD calculations using dyn file

My guess is you should have saved the original dyn.h5 with a different name and used that as a restart file, otherwise DYNAMIX is probably overwriting the file before trying the restart.