# Random docking fails in it0 and question about running job via batch system **URL:** \ **Category:** HADDOCK\ **Created:** [March 27, 2020, 6:33am UTC](https://ask.bioexcel.eu/t/random-docking-fails-in-it0-and-question-about-running-job-via-batch-system/1868 "2020-03-27T06:33:34Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![zsip029](https://avatars.discourse-cdn.com/v4/letter/z/ce7236/32.png) [@zsip029](https://ask.bioexcel.eu/u/zsip029)\ **Post date:** [March 27, 2020, 6:33am UTC](https://ask.bioexcel.eu/t/random-docking-fails-in-it0-and-question-about-running-job-via-batch-system/1868/1 "2020-03-27T06:33:34Z")
Hi, Admin! I come here for help again. Now I have two questions to ask: 1. protein-protein random docking fails (a) Firstly, I chose surface residues with relative SASA larger than 50% as active site. In my experience, the choice of active sites in random docking doesn’t affect on the restraints in simulation So I choice the active site casually. Is my understanding right?? (b) Secondly, I modified ranair=true in run.cns for random docking. Other modifications include iseed, number of structures in each stage. (50000 in it0, 400 in it1 and it1/water) © This works for other proteins. But one of cases fails in it0 stage with error that “**HADDOCK cannot continue due to too many (\>20%) failed structures in it0 The following structures could not be docked**”. But their \*.out.gz file seems normal, although it ends with these output: ```auto PRIEND: 1 levels not terminated LEVEL= 1 KEY=CNSsolve> ACTION=GO ============================================================ Maximum dynamic memory allocation: 973500288 bytes Maximum dynamic memory overhead: 2656 bytes ``` But, this also appears in the successed jobs. The failed job’s docked complex is also normal. So what is the reason why they fail? Is there any other output infomation I shoud check. **(d)** I also check other successed cases in which there are also about hundards of failed jobs less than 20%. So it can go on. 1. Is it possible triggered by job system. I modify jobmax[‘it0’]= 200, jobmax[“it1”] = 10 in QueueSubmit.py and QueueSubmit\_cont.py. And I want to use 40 cpus to run the job. So I modify cpunumber\_1=8000. t {===\>} queue\_1="/home/work/dock1/run2/ssub"; {===\>} cns\_exe\_1="/home/soft/haddock/cns\_solve\_1.3/intel-x86\_64bit-linux/bin/cns"; {===\>} cpunumber\_1=8000; The question description is really long. Thanks for your time and patience. ---
**Author:** ![zsip029](https://avatars.discourse-cdn.com/v4/letter/z/ce7236/32.png) [@zsip029](https://ask.bioexcel.eu/u/zsip029)\ **Post date:** [March 27, 2020, 1:00pm UTC](https://ask.bioexcel.eu/t/random-docking-fails-in-it0-and-question-about-running-job-via-batch-system/1868/2 "2020-03-27T13:00:45Z")
In my other test on the same docking case, it still fails with error in log file: ```auto HADDOCK cannot continue due to failed structures in it0 HADDOCK could not copy failed structures from previous iteration The following structures could not be docked: ``` ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [March 27, 2020, 1:16pm UTC](https://ask.bioexcel.eu/t/random-docking-fails-in-it0-and-question-about-running-job-via-batch-system/1868/3 "2020-03-27T13:16:15Z")
Are all structures failing at it1? Do check the content of an it1 out file in the run directory and search for error messages (start from the end of the file) ---
**Author:** ![zsip029](https://avatars.discourse-cdn.com/v4/letter/z/ce7236/32.png) [@zsip029](https://ask.bioexcel.eu/u/zsip029)\ **Post date:** [March 27, 2020, 2:35pm UTC](https://ask.bioexcel.eu/t/random-docking-fails-in-it0-and-question-about-running-job-via-batch-system/1868/4 "2020-03-27T14:35:01Z")
No, it fails at it0 stage. How can I control the number of job submitted so that it only run on 40 cores, rather than submiting hundards of submited jobs. Now I have set jobmax[“it0”]=50 and cpunumber\_1=2000 which equals 50 jobs/per \* 40 cores in my understanding. But more than 40 jobs were submited simultaneously. ---
**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\ **Post date:** [March 27, 2020, 5:27pm UTC](https://ask.bioexcel.eu/t/random-docking-fails-in-it0-and-question-about-running-job-via-batch-system/1868/5 "2020-03-27T17:27:49Z")
> No, it fails at it0 stage. > How can I control the number of job submitted so that it only run on 40 cores, rather than submiting hundards of submited jobs. Now I have set jobmax[“it0”]=50 and cpunumber\_1=2000 which equals 50 jobs/per \* 40 cores in my understanding. But more than 40 jobs > were submited simultaneously. cpunumber effectively defines the number of jobs your are sending to the batch system, each job will compute 50 models (the jobmax[“it0”] value And each jobs uses only one core. Did you check for error messages in the output files?