Dear Marian, Thanks for your report. I'm sorry you're having to deal with this problem. There is nothing wrong with your machine; this is an identified bug and we're working towards fixing it. In the meantime, the only workaround I can think of is to roll CCP4 back to a previous update, e.g. 015. I will keep you posted, Jon
On Fri, 5 Apr 2024 at 12:54, Marian Oliva <mar...@cib.csic.es> wrote: > Dear list, > > > > I have a problem running the Validation and Analysis in Refmac and I would > really appreciate any feed-back from your side. > > > > I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4). > > > > Last time I was using Refmac was in November 2023. At the time, I posted > in the list an error with the CCP4i2 interface (no responding) that I > solved by turning off the 3D picture in the reports (as kindly suggested by > Stuart McNicholas). > > > > Now, despite the 3D picture in the reports is off, I still experience > ‘some delays’ on the interface response, though this is not a major issue. > > > > The real problem I’m experiencing is that after a (apparent) normal > termination of Refmac (no sign of warnings or error messages), I find no > results from the Multimeric validation. > > > > Navigating through the jobs folders I have found that in job2 (which I > guess correspond to the validation) there is: > > - no prosmart related files (.out, .pdb, .py). > > - the tables_as_csv_files folder is empty. > > - there is no molprobity.log file. Instead, there is a log_mtzjoin.txt > file but it does not highlight any warning or error either. > > - the program.xml file only contains the heather but otherwise, it is > blank (which I guess this is the reason it is not running). > > - also, in the param.xml file I found that there are 2 sets of input data > (instead of one and I don’t know why), where: > > - There is no dbFileID for the input F-SIGF data (in any of them) > > - In the first one the XYZIN is the XYZIN-coordinated.pdb (instead > of the xyzout_prosmart_refmac.pdb) and in the second it is the > xyzout_prosmart_refmac.pdb) > > > > Checking the terminal while running refmac I saw the following error > message that appears just after refmac window state ‘The job is finished’. > This error repeats multiple times, with variations in the > .WebGL-alphanumerical code, from time to time and ends as follows. > > > > [3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc(12701)] > [.WebGL-0x23e9d90]GL ERROR :GL_INVALID_VALUE : glVertexAttrib4f: index out > of range > > <--- Last few GCs ---> > > [4500:0xc3700000000] 177121 ms: Scavenge 2518.8 (2529.1) -> 2510.8 > (2529.1) MB, 0.2 / 0.0 ms (average mu = 0.980, current mu = 0.948) > allocation failure > [4500:0xc3700000000] 177148 ms: Scavenge 2518.8 (2529.1) -> 2510.8 > (2529.1) MB, 0.2 / 0.0 ms (average mu = 0.980, current mu = 0.948) > allocation failure > [4500:0xc3700000000] 177175 ms: Scavenge 2518.8 (2529.1) -> 2510.8 > (2529.1) MB, 0.2 / 0.0 ms (average mu = 0.980, current mu = 0.948) > allocation failure > > > <--- JS stacktrace ---> > > [4500:4500:0405/112334.605730:FATAL:memory.cc(38)] Out of memory. size=0 > > > > > > Because at the end there is an ‘out of memory’ message, I have increased > the ram of my computer from 16GB to 32GB but the problem persists. Another > piece of info is that my computer has 8 CPU but when running CCP4i2 it only > uses one. > > > > Does anybody have an idea of which could be the problem? > > > > Best regards, > > Marian > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- Dr Jon Agirre (He/Him) Royal Society University Research Fellow (assistant professor) Main editor at Acta Crystallographica Section F: Structural Biology Communications CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
