Issue with fragment job submission in Q-Chem 5.0.1 EDA calculations

Questions
#1

$molecule
1 1

0 1

C -0.34726700 -1.90963000 -1.28567400
H 0.53326300 -2.53579600 -1.38668400
H -1.22968200 -2.39892700 -0.88844600
C -0.50759800 -0.78264000 -2.10767100
H 0.25583300 -0.56061300 -2.84628800
H -1.51653500 -0.47518400 -2.36979400

1 1

C -2.63226200 0.55194200 0.03031600
C -2.12427200 1.81843800 -0.45374000
H -2.31759400 -0.45153600 2.01075000
C -1.28659700 2.41718700 0.57601300
C -1.35461400 1.51672700 1.70259700
C -2.09884300 0.36811800 1.34272100
C 1.50613600 1.87420600 -1.56842200
C 2.22358500 0.65988700 -1.44401600
C 2.66879000 0.51566700 -0.09584300
C 2.15574300 1.65441400 0.63621100
C 1.39334000 2.49722000 -0.27146000
C -3.51084500 -0.25272200 -0.76126000
H -4.55375800 -0.32596100 -2.62342900
C -3.86306700 0.24244900 -2.00771300
H -3.70877200 1.83355300 -3.46416100
C -3.37482700 1.48485400 -2.49146400
H -2.19103300 3.22999100 -2.11913600
C -2.51275900 2.26415700 -1.74930100
H 2.20573300 2.68413000 2.56044800
C 2.49325700 1.79453200 2.01460100
H 3.53801100 0.92847900 3.65996500
C 3.25403500 0.81909100 2.61744600
H 4.34365800 -1.03965600 2.41358800
C 3.72127300 -0.31409000 1.89856700
C 3.47006100 -0.48522800 0.54881100
H 2.45943500 -0.00673500 -2.26123300
Si 0.05566800 3.73159000 0.28036800
C 0.49756000 4.69756500 1.83381300
H -0.26740900 5.46650000 1.99746600
H 1.45536900 5.21271300 1.69321600
H 0.56164700 4.10395300 2.74744800
C -0.38170800 4.99496900 -1.04360900
H -0.48181800 4.59666900 -2.05455300
H 0.40627700 5.75762000 -1.06950400
H -1.31844100 5.50100600 -0.78089000
C 0.37991900 -1.64163500 0.83603800
H 0.49116200 -0.76276200 1.55588100
Zr 0.01740800 0.43787400 -0.12296400
C -0.46873400 -2.70461300 1.52280100
H -0.35573500 -3.64367600 0.96701800
H -1.53256200 -2.44765700 1.47708900
C -0.04613900 -2.92714700 2.98285900
H -0.63477500 -3.72853000 3.44154100
H 1.01308900 -3.20047400 3.05211900
H -0.19512800 -2.01702400 3.57746700
H 1.39562600 -2.00309300 0.67228900
C -0.82359700 1.71559600 3.10050700
H -1.28949200 2.59727200 3.55361900
H -1.07113000 0.84877800 3.72066300
H 0.25784800 1.84963600 3.14457200
C 0.98056100 2.38033800 -2.88895100
H 1.38608400 3.37420100 -3.10384200
H 1.28576500 1.71095300 -3.69823000
H -0.11048100 2.45254600 -2.91731400
C 3.98045600 -1.66197800 -0.19416200
C 4.58053700 -1.52509000 -1.45859300
C 3.88318800 -2.94912600 0.36518600
C 5.05580800 -2.64151700 -2.14562900
H 4.71134300 -0.53517200 -1.88531100
C 4.35315300 -4.06599200 -0.32592000
H 3.42907900 -3.07286600 1.34511500
C 4.93714700 -3.91629500 -1.58569900
H 5.53031700 -2.51465800 -3.11450200
H 4.26501500 -5.05223100 0.12080900
H 5.30549200 -4.78494000 -2.12340800
C -3.97835200 -1.57714500 -0.28578300
C -3.90964100 -2.69155800 -1.14055400
C -4.47894900 -1.75864900 1.01511800
C -4.30537300 -3.95457200 -0.69966300
H -3.52633200 -2.56607100 -2.14983800
C -4.87889600 -3.02109100 1.45316700
H -4.58669000 -0.90147600 1.67293700
C -4.78546100 -4.12443900 0.60093100
H -4.23818600 -4.80510000 -1.37198600
H -5.27456900 -3.14109300 2.45765700
H -5.09409600 -5.10719900 0.94482800
$end

$rem
JOBTYPE EDA
EDA2 2
METHOD M062X
BASIS def2-TZVPP
Solvent_method SMD
SYMMETRY false
MEM_TOTAL 4000
MEM_STATIC 1000
MAX_SUB_FILE_NUM 16000
BASIS_LIN_DEP_THRESH 6
THRESH 14
SCF_CONVERGENCE 8
GEN_SCFMAN TRUE
MAXSCF 200
SCF_GUESS FRAGMO
XC_GRID 000099000590
NL_GRID 1
FD_MAT_VEC_PROD false
$end

“I am performing an ALMO-EDA (Energy Decomposition Analysis) calculation using Q-Chem 5.0.1. The job fails when spawning the sub-jobs for molecular fragments. Specifically, while Fragment 0 (Frg1) seems to initialize, the process fails for Fragment 1 (Frg2) with the error: ‘ReadJobInputs output failure!!’ and ‘Error opening input stream for input #0’.”
“Looking at the log file, it appears that the environment variables for the scratch directory are being corrupted or recursively appended. The log shows: calling putenv with: QCSCRATCH=/state/partition1/tmp/wangxiao/95318/local//state/partition1/tmp/wangxiao/95318/ This path is invalid due to the repeated directory string. I suspect this is a bug in how Q-Chem 5.0 handles path inheritance for fragmented jobs in EDA mode when QCSCRATCH and QCLOCALSCR are both defined or passed via command line arguments.” Thank you for your reply.
"The following is an excerpt from the Q-Chem log file.
Attempting to make child job directory: /state/partition1/tmp/wangxiao/89258/qchem2171311//Frg1/
Attempting to make child job directory: /state/partition1/tmp/wangxiao/89258/qchem2171311//Frg2/
Creating input file /state/partition1/tmp/wangxiao/89258/qchem2171311/Frg1.input
using default PutDataFrgm: nothing
calling putenv with: QCSCRATCH=/state/partition1/tmp/wangxiao/89258/qchem2171311/
calling putenv with: QCLOCALSCR=/state/partition1/tmp/wangxiao/89258/qchem2171311/
Spawning Job For Fragment 0
/home/liuzhen/0_script/qchem/qchem/bin/xr.csh /state/partition1/tmp/wangxiao/89258/qchem2171311/Frg1.input /dev/null Frg1
/home/liuzhen/0_script/qchem/qchem/exe/qcprog.exe_s /state/partition1/tmp/wangxiao/89258/qchem2171311/Frg1.input /state/partition1/tmp/wangxiao/89258/qchem2171311//Frg1/ frag.log
Done Job For Fragment 0
calling putenv with: QCSCRATCH=/home/wangxiao/Q-Chem/8_Ethylene_TS
calling putenv with: QCLOCALSCR=/state/partition1/tmp/wangxiao/89258

Q-Chem fatal error occurred in module /scratch/svnadmin/18824_zgan/qchem/libmdc/newfileman.C, line 293:

Error reading in TMP file 659/0 (80)

remove work dirs /state/partition1/tmp/wangxiao/89258/qchem2171311.0 – /state/partition1/tmp/wangxiao/89258/qchem2171311.0
rm -rf /state/partition1/tmp/wangxiao/89258/qchem2171311.0
rm -rf /state/partition1/tmp/wangxiao/89258/qchem2171311

#2

If your hypothesis is correct then presumably it should fail for any of the (much smaller and simpler) EDA jobs that are in the manual. Have you confirmed that is the case?

#3

$molecule
1 4

0 1
H -3.31746900 4.66482100 -0.68656700
C 1.39494200 2.99588900 -0.99169700
C -3.46958600 3.58890900 -0.80204600
C -4.81974100 1.72548200 -1.55281000
C -2.68662000 1.31488000 -0.46266700
C -2.49930500 2.69930600 -0.32940200
H -5.38362600 3.80224500 -1.78579400
H 0.31026700 3.00213700 -0.88193600
H 4.13942100 1.06086800 -0.33267900
H -3.89129500 -3.41278400 3.82675700
H -4.01897800 -0.24223900 -1.18670400
C 2.36970500 -0.34838900 1.36720300
C 2.14446100 1.91538800 -0.49479500
C 3.53846300 1.90198700 -0.68437500
C 3.87175600 -1.69483700 3.31746700
H 4.45584600 -2.21671300 4.07941300
C 4.16920500 2.97089500 -1.32755200
H 5.25324400 2.95405600 -1.46362700
C -3.85616100 0.83312400 -1.08012200
C -4.62799300 3.10526200 -1.41549400
C -1.84322600 -2.34470200 1.31883200
P 1.26688100 0.44409100 0.14310300
H 4.68078300 0.25097300 3.81184600
C -2.41352800 -3.20226400 2.26187400
H -4.71622800 -1.07059900 3.60904500
C -3.90707800 -1.42767600 2.96746600
H -1.04260800 -2.71404300 0.67108300
H 3.91752200 4.88981900 -2.29371300
C 3.42023000 4.05481700 -1.79439600
H -5.72475300 1.34219900 -2.03018700
N -0.19969000 0.93529000 0.92270100
P -1.42260700 0.09309900 0.03675300
C -2.29584800 -1.01947300 1.19878400
C -3.44339200 -2.74222600 3.08934900
H -1.60402100 3.09065200 0.15316800
H -2.05815400 -4.23182900 2.34794800
H 1.43866200 4.90217400 -2.00089100
C 2.03095900 4.06282300 -1.62846700
H 2.91072100 -3.49523100 2.59583900
C 3.00443900 -2.41210400 2.48818500
C -3.33917800 -0.56756900 2.02490000
H -3.71073500 0.45544900 1.93171500
C 3.99863500 -0.30894100 3.16762500
H 1.59193000 -2.31106300 0.86285400
C 2.26075900 -1.74210000 1.51423400
H 3.36025200 1.44601600 2.09478400
C 3.25246300 0.36450100 2.19874600
C -0.41922600 1.60440400 2.23660200
C 0.38269500 2.89869300 2.35370300
C -0.17014900 0.66494900 3.42197400
H -1.49067100 1.86574400 2.23775800
H 0.17130500 3.38079600 3.32048700
H 1.46491100 2.70595300 2.30842300
H 0.13594600 3.61084600 1.55350600
H 0.89828300 0.44046300 3.54497800
H -0.52314300 1.14119600 4.35025500
H -0.71033300 -0.28395800 3.30086600

1 4
Cr 0.10950200 -0.92042200 -1.61588900
H -0.35791000 -1.71815100 -4.36099400
H 0.74555500 -1.70160200 -2.90757900
H -2.22586000 -2.27701900 -1.99854800
H -2.19032400 -0.76322700 -3.03991900
C -0.51248600 -2.13707600 -3.35379200
C -1.62025100 -1.59354400 -2.60714400
C 2.11966600 -1.73510200 -2.30020200
C -0.17058200 -3.62874400 -3.26005400
C 1.32915400 -3.92400300 -3.41669400
C 2.19304600 -3.27261500 -2.32318100
H 2.54601900 -1.31224100 -3.22727200
H 2.72079400 -1.33379100 -1.47310700
H -0.51744300 -4.01650100 -2.28446100
H -0.74860800 -4.17122600 -4.02756900
H 1.48686900 -5.01458800 -3.40936100
H 1.66929300 -3.56970900 -4.40743300
H 1.87956500 -3.67336300 -1.33980000
H 3.24327300 -3.59095200 -2.45032800
$end

$rem
JOBTYPE EDA
EDA2 2
METHOD M06L
BASIS def2-TZVPP
Solvent_method SMD
SYMMETRY false
MEM_TOTAL 4000
MEM_STATIC 1000
MAX_SUB_FILE_NUM 16000
BASIS_LIN_DEP_THRESH 6
THRESH 14
SCF_CONVERGENCE 8
GEN_SCFMAN TRUE
MAXSCF 200
SCF_GUESS FRAGMO
XC_GRID 000099000590
NL_GRID 1
FD_MAT_VEC_PROD false
$end

$solvent
Dielectric 2.02
$end

“I have tested a different system using the exact same script and environment, and it runs perfectly fine—the second fragment is recognized without any issues. However, with this specific ethylene transition state system, it fails to read Fragment 2. I am wondering if the error is triggered by the specific molecular geometry or the fragment definitions in this input file rather than the environment setup.”

#4

Your original job runs successfully with the latest version of Q-Chem (v. 6.4.1). You will need to contact Q-Chem technical support if you want specific help with a much older version.