bmin returned non-zero exit status 126

[youngbee12]

[KristapsE]

It looks like DP4 is trying to launch MacroModel bmin executable, but can't do that because of insufficient file permissions. Please try launching it manually in a new terminal with '/media/young_bee123/AnGEL/schor/bmin AT1_1'

If it doesn't work, then either your user is not allowed to access the file, or perhaps the bmin is not allowed to be executed. This can be fixed with running "chmod +x bmin" in the schrodinger folder

[youngbee12]

Thanks for your advice.But i can't find a file called bmin.I change bmin into maestro,then it runs maestro.After that I don’t know what to do.

[KristapsE]

What I meant is - can you find the bmin executable in your schrodinger folder? If it's there you should be able to launch it manually from command line/terminal, if your user and the file have the right permissions.

[youngbee12]

I can't find bmin executable in my schrodinger folder....

[KristapsE]

That would suggest to me that you don't have MacroModel installed. Do you have the free Maestro version, or the full commercial Schrodinger Suite? MacroModel is included only in the paid Schrodinger Suite.

The DP4-AI will not work without either MacroModel or TINKER as the molecular mechanics software.

[youngbee12]

Ok i will buy one，thanks for your help

[youngbee12]

what does“returned non-zero exit status 1”mean？

[KristapsE]

Still seems to be a problem with your MacroModel. Have you tried running bmin manually from command line? The output files might contain some error messages.

[youngbee12]

Cannot open shared object file, but I found this file (libxxxx.so)in another directory.

[KristapsE]

That is definitely a problem with your Schrodinger installation. Are you saying you have libcoordgenlibs.so somewhere else in schrodinger folder? It should be either in internal or mmshare subfolder, I think...

Maybe try looking into this GitHub which seems relevant? https://github.com/schrodinger/coordgenlibs

Also could try installing this package, or it's ubuntu analog. https://packages.debian.org/sid/libschroedinger-coordgenlibs1

[WeiYongqiang55]

what does“returned non-zero exit status 1”mean？

I met same problem, do you solved this problem?could you please tell how ? thank you so much

[WeiYongqiang55]

Cannot open shared object file, but I found this file (libxxxx.so)in another directory.

I have bmin & could could run it (chem-env) root@ubuntu:/app/schrodinger2018-1# ./bmin

Usage: bmin [OtherOptions] [JobOptions] [DiagnosticOptions]

The name of the .com file leaving out the ".com". Not needed or used if -TEST or -HELP are specified. Other Options: -------------- -h, -help, -HELP Print this message and exit. -DEBUGGER Run bmin in the foreground with specified debugger. -TEST Run the standard test suite (jobname not needed). -DEV_TEST Run the developers version of the standard test suite (jobname not needed). Turns on -TEST. Job Options: ------------ -DEBUG Show details of operation of the toplevel scripts. -HOST or -HOST or -HOST "hostname1:nproc1 hostname2:nproc2 ... hostnameN:nprocN" Distribute the job over the specified hosts. The driver job is run on the first host specified. If -SUBHOST is used to specify the hosts for the subjobs, the -HOST option only specifies the host for the driver. -HOSTFILE The name of the host file to use for this run. -LOCAL Do not use a temporary directory for job files. Keep files in the launch directory. -NICE Run the job at reduced priority. -NOJOBID Do not use job control and print bmin messages to the screen. -PROJ Assign job to a Maestro project . -TMPDIR The name of the directory used to store files temporarily during a job. -USER Launch job as user . -WAIT Do not return a prompt until the job completes. -RESTART Restart the previously failed parent job. This facility works only for local jobs. -ARCH The platform tag must match (e.g. mips3). -COMPAT Require compatiblity with executables in . -REL The version number must match (e.g. 80 or 80015). -VER Exec directory pathname must match . ** Distributed job options: -SUBHOST or -SUBHOST or -SUBHOST "hostname1:nproc1 hostname2:nproc2 ... hostnameN:nprocN" Run the subjobs on the specified hosts. The driver is run on the host specified with -HOST. -NJOBS Number of subjobs to create. If this option is omitted, -NJOBS will be set to the number of cpus requested with -SUBHOST option. -JOBCTS Ensure that each subjob has no more than this many structures to process. Defaults to 10000. -STRICT_END Terminate if any of the subjobs dies. -MAX_RETRIES Number of allowed retries per subjob. -first First structure to process. -last Last structure to process. -OUTPUT_ORG Produce more than one output structure file. If option is BY_SUBJOB produce one output file for each subjob. Otherwise create a new directory called: option and create separate output files for each input ligand within this new directory. -NC or -nc Do not clean up by removing intermediate files. By default many intermediate job files are removed. -nx Do not run jobs, but create specified subjob directories and input structures. -j Only run specified subjobs. For example of range values; 10 job number 10 1:15 job numbers 1 to 15 "1, 5, 10" job numbers 1, 5, and 10 "1:15, 18" job numbers 1 to 15 and 18 "1:5, 15:20" job numbers 1 to 15 and 15 to 20 Diagnostic Options: (Provide information but the program will not run). ------------------- -ALL Ignore platform compatibility (list all platforms). -ENTRY List the relevant host entry(s) from the hosts file. -HOSTS List the hosts available for remote jobs. -LIST List all the platform-compatible versions of product. -WHICH Report the product exec directory and MMSHARE_EXEC. -WHY Show details of how the selected exec dir was chosen. (chem-env) root@ubuntu:/app/schrodinger2018-1#

[KristapsE]

Are you running the latest version of DP4-AI? The latest update was released just 2 days ago, which have introduced some improvements in file location specification, both for executables and the input files. Could you please paste the output from DP4-AI? Your bmin installation looks fine, so it must be a file location issue, but difficult to say anything more specific without the error messages.

[youngbee12]

My computer is paralyzed, so I am still recovering my data.Thank you for helping me solve the problem，I will try later1

[youngbee12]

what does“returned non-zero exit status 1”mean？

I met same problem, do you solved this problem?could you please tell how ? thank you so much

Sorry i haven't solved

[WeiYongqiang55]

Are you running the latest version of DP4-AI? The latest update was released just 2 days ago, which have introduced some improvements in file location specification, both for executables and the input files. Could you please paste the output from DP4-AI? Your bmin installation looks fine, so it must be a file location issue, but difficult to say anything more specific without the error messages.

I try the new code ,and met some other bug,I open a new issue,could you please have a look ?thank you

[WeiYongqiang55]

Are you running the latest version of DP4-AI? The latest update was released just 2 days ago, which have introduced some improvements in file location specification, both for executables and the input files. Could you please paste the output from DP4-AI? Your bmin installation looks fine, so it must be a file location issue, but difficult to say anything more specific without the error messages.

well I use old code DP4, output is exectly seem with https://user-images.githubusercontent.com/61130599/81362590-c690b580-9113-11ea-98ac-c4ad7338b4af.png

[KristapsE]

I would probably try reinstalling Schrodinger and see if you can run bmin manually from either command line or the Maestro interface. But as it seems as an issue with MacroModel, and not with DP4-AI, I am going to close this issue.