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emartineznunez / AutoMeKin

Automated discovery of reaction Mechanisms and Kinetics
https://emartineznunez.github.io/AutoMeKin/
MIT License
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strange 'rm' command after one iter #1

Open shuaijiang-ustc opened 2 years ago

shuaijiang-ustc commented 2 years ago

Hi, recently I installed AutoMeKin following the instructions of building from sources. Then after "module load amk/2021", I ran "nohup llcalcs.sh FA.dat 50 10 20 >llcalcs.log 2>&1 &" for test. Here is the output in llcalcs.log: nohup: ignoring input

===================================

       AutoMeKin2021           

    revision number 1135

===================================

Number of iterations = 10 Tasks per iteration = 50

GENERAL
Name of the system = FA Charge = 0 Number of atoms = 5 Low-level MD simul. = mopac pm7 Low-level TS optim. = mopac pm7

METHOD
MD sampling BBFS algorithm details: Attempts/single path = 1 All atoms are excited Temperature (K) = Automatically selected Number of trajs = 10 Total time (fs) = 500

SCREENING
Min imag freq (cm-1) = 200 Max energy (kcal/mol) = 225 Max value of MAPE = 0.008 Max value of BAPE = 2.5

CALCULATIONS START HERE

=======================

  Iter: 1/10

=======================

Running TS search time: 69 s Running IRC
time: 12 s New TSs found: 8 Running min opt
time: 14 s Building network rm: cannot remove ‘/bio_data/caohui/scq/canceljob.sh’: Permission denied rm: cannot remove ‘/bio_data/caohui/scq/down1.sh’: Permission denied rm: cannot remove ‘/bio_data/caohui/scq/trim_galore.sh’: Permission denied rm: cannot remove ‘/bio_data/caohui/scq/reads2.sh’: Permission denied rm: cannot remove ‘/bio_data/caohui/scq/submit_bam_reads.py’: Permission denied ...

After one iter, 'rm' command was run very strangely and also dangerously as it intended to remove all files in the root dir. Then I shut down all the processes. So I am wondering what's going on with this. Thanks!

shuaijiang-ustc commented 2 years ago

Hi, I checked the workflow and found that the issue is probably caused by this line in conf_isomer_ts.sh: tmp_files=(ConnMat deg.out deg_form.out deg mingeom ScalMat sprint.out cits c_i_ts fort. ${working}/data ${working}diag), where ${working}/_data accidentally covers my root directory called '/bio_data/...', so I deleted ${working}/_data in the line and everything works fine. But I am still wondering why ${working} is empty and whether there is the similar issue in other .sh files. Thanks.

emartineznunez commented 2 years ago

Hi, Directory ${working} should not be empty. The path would be: ${tsdirll}/working. If there is a conflict with the name, perhaps you can change it in AutoMeKin shell scripts. All the best, Emilio

shuaijiang-ustc commented 2 years ago

Hi, Emilio, I see, many thanks for the reply!