Hello All, I've recently solved a membrane protein structure largely with the help of phenix refine. I also have been using the autobuild programs recently for ligand fitting and whatnot. The program during this time has been running flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR spontaneously started throwing this error. (boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Memtest 86 says my RAM is good. I have reinstalled phenix and am still getting the same error. I can't seem to find any other information on this error (segmentation faults are tricky I know) and am just wondering if anyone else has seen or solved this type of problem, thanks for your help. Andrew Waight Wang Lab Skirball Institute of Biomolecular Medicine NYU school of medicine </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>
Hi Andrew,
I've recently solved a membrane protein structure largely with the help of phenix refine. I also have been using the autobuild programs recently for ligand fitting and whatnot. The program during this time has been running flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR spontaneously started throwing this error.
(boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27]
What version of phenix do you have (phenix.version)? Which phenix installer tar file did you use? Did that same version work before? Are you running automatic OS updates? Do you have a 32-bit or 64-bit OS (uname -m)?
Memtest 86 says my RAM is good.
Yes, it is almost certainly a software problem, but what exactly is difficult to know.
I have reinstalled phenix and am still getting the same error. I can't seem to find any other information on this error (segmentation faults are tricky I know) and am just wondering if anyone else has seen or solved this type of problem, thanks for your help.
Could you try installing from sources? This is not guaranteed to help, and you'll get slower solve and resolve (gfortran optimizes very poorly), but it would be another data point for us. To get the sources: https://www.phenix-online.org/download/phenix/nightly/?version=1.4-129&show_source=1 Replace the version number with the one you have already. You will need the password again (which has just changed; you probably have to re-request). Don't forget to add --nproc=8 or similar to the ./install command, to speed up the installation. Ralf
Thanks for your help Ralf, Just to close out this issue, after trying everything suggested... reinstalls etc etc, and trying to track down the call backs for approximately two days, I fixed the problem. I simply dialed back the overclock on my rig a little (duh) I guess phenix just taxes the cpu a little bit more than all my other stress tests (overnight ray traces and other dual 99% CPU o/n processes worked fine). Anyway I apologize that the solution was so embarrassingly simple. Drew Waight P.S. I like the new interface exhibited in the nightly builds, but does one need to manually configure an AutoBuild through the deprecated GUI (or command line) following an AutoMR run? -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Ralf W. Grosse-Kunstleve Sent: Monday, August 03, 2009 10:51 AM To: [email protected] Subject: Re: [phenixbb] Segmentation Fault Hi Andrew,
I've recently solved a membrane protein structure largely with the help of phenix refine. I also have been using the autobuild programs recently for ligand fitting and whatnot. The program during this time has been running flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR spontaneously started throwing this error.
(boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27]
What version of phenix do you have (phenix.version)? Which phenix installer tar file did you use? Did that same version work before? Are you running automatic OS updates? Do you have a 32-bit or 64-bit OS (uname -m)?
Memtest 86 says my RAM is good.
Yes, it is almost certainly a software problem, but what exactly is difficult to know.
I have reinstalled phenix and am still getting the same error. I can't seem to find any other information on this error (segmentation faults are tricky I know) and am just wondering if anyone else has seen or solved this type of problem, thanks for your help.
Could you try installing from sources? This is not guaranteed to help, and you'll get slower solve and resolve (gfortran optimizes very poorly), but it would be another data point for us. To get the sources: https://www.phenix-online.org/download/phenix/nightly/?version=1.4-129&show_source=1 Replace the version number with the one you have already. You will need the password again (which has just changed; you probably have to re-request). Don't forget to add --nproc=8 or similar to the ./install command, to speed up the installation. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================
P.S. I like the new interface exhibited in the nightly builds, but does one need to manually configure an AutoBuild through the deprecated GUI (or command line) following an AutoMR run?
I'm not sure if I understand the question, but you should be able to turn off building in AutoMR, and run AutoBuild through the new GUI afterwards. The replacement for the AutoMR GUI should be available sometime next month, I hope. -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]
participants (3)
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Nathaniel Echols -
Ralf W. Grosse-Kunstleve -
Waight, Andrew