Re: [gmx-users] Failed to lock: md.log. No locks available.
On 13/01/2012 7:08 PM, lina wrote: Hi, Failed to lock: md.log. No locks available. mdrun locks various files at various points. If it can't then GROMACS won't continue, but the problem lies with the file system, and not with GROMACS. Possibly some phantom process still thinks it owns the file. Mark still the same problem I met before, once I terminated, resume not work, there is a md.log file. $ mount /dev/sda1 on / type ext3 (rw) none on /proc type proc (rw) none on /sys type sysfs (rw) none on /dev/pts type devpts (rw,gid=5,mode=620) usbfs on /proc/bus/usb type usbfs (rw) none on /dev/shm type tmpfs (rw) none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) The /home is mounting on the last one. CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz Memory: 114GB RAM HDD Size: 744GB OS: CentOS 4 (64-bits) Thanks for any suggestions, any additional info you need please let me know, Best regards, -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Failed to lock: md.log. No locks available.
On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham wrote: > On 13/01/2012 7:08 PM, lina wrote: >> >> Hi, >> >> Failed to lock: md.log. No locks available. > > > mdrun locks various files at various points. If it can't then GROMACS won't > continue, but the problem lies with the file system, and not with GROMACS. > Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, > > Mark > > >> >> still the same problem I met before, >> >> once I terminated, resume not work, there is a md.log file. >> >> $ mount >> /dev/sda1 on / type ext3 (rw) >> none on /proc type proc (rw) >> none on /sys type sysfs (rw) >> none on /dev/pts type devpts (rw,gid=5,mode=620) >> usbfs on /proc/bus/usb type usbfs (rw) >> none on /dev/shm type tmpfs (rw) >> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) >> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) >> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs >> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) >> >> The /home is mounting on the last one. >> >> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz >> Memory: 114GB RAM >> HDD Size: 744GB >> OS: CentOS 4 (64-bits) >> >> Thanks for any suggestions, >> >> any additional info you need please let me know, >> >> Best regards, > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Failed to lock: md.log. No locks available.
There is a solution in this mailing list sometime before: mv md.log to some other folder and copy it back. Jianguo From: lina To: Discussion list for GROMACS users Sent: Friday, 13 January 2012, 18:51 Subject: Re: [gmx-users] Failed to lock: md.log. No locks available. On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham wrote: > On 13/01/2012 7:08 PM, lina wrote: >> >> Hi, >> >> Failed to lock: md.log. No locks available. > > > mdrun locks various files at various points. If it can't then GROMACS won't > continue, but the problem lies with the file system, and not with GROMACS. > Possibly some phantom process still thinks it owns the file. It's something relevant to the server. I am not experienced to figure it out even did some rough try. will drop an email to administrator. Thanks, > > Mark > > >> >> still the same problem I met before, >> >> once I terminated, resume not work, there is a md.log file. >> >> $ mount >> /dev/sda1 on / type ext3 (rw) >> none on /proc type proc (rw) >> none on /sys type sysfs (rw) >> none on /dev/pts type devpts (rw,gid=5,mode=620) >> usbfs on /proc/bus/usb type usbfs (rw) >> none on /dev/shm type tmpfs (rw) >> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) >> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) >> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs >> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) >> >> The /home is mounting on the last one. >> >> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz >> Memory: 114GB RAM >> HDD Size: 744GB >> OS: CentOS 4 (64-bits) >> >> Thanks for any suggestions, >> >> any additional info you need please let me know, >> >> Best regards, > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Failed to lock: md.log. No locks available.
On Fri, Jan 13, 2012 at 7:04 PM, Jianguo Li wrote: > There is a solution in this mailing list sometime before: > mv md.log to some other folder and copy it back. > Jianguo I tried, not work. Thanks, > > From: lina > To: Discussion list for GROMACS users > Sent: Friday, 13 January 2012, 18:51 > Subject: Re: [gmx-users] Failed to lock: md.log. No locks available. > > On Fri, Jan 13, 2012 at 4:57 PM, Mark Abraham > wrote: >> On 13/01/2012 7:08 PM, lina wrote: >>> >>> Hi, >>> >>> Failed to lock: md.log. No locks available. >> >> >> mdrun locks various files at various points. If it can't then GROMACS >> won't >> continue, but the problem lies with the file system, and not with GROMACS. >> Possibly some phantom process still thinks it owns the file. > > It's something relevant to the server. > I am not experienced to figure it out even did some rough try. > will drop an email to administrator. > > Thanks, > >> >> Mark >> >> >>> >>> still the same problem I met before, >>> >>> once I terminated, resume not work, there is a md.log file. >>> >>> $ mount >>> /dev/sda1 on / type ext3 (rw) >>> none on /proc type proc (rw) >>> none on /sys type sysfs (rw) >>> none on /dev/pts type devpts (rw,gid=5,mode=620) >>> usbfs on /proc/bus/usb type usbfs (rw) >>> none on /dev/shm type tmpfs (rw) >>> none on /proc/sys/fs/binfmt_misc type binfmt_misc (rw) >>> sunrpc on /var/lib/nfs/rpc_pipefs type rpc_pipefs (rw) >>> honeydewlocal:/vol/hpc_vol/HomeHPC on /home type nfs >>> (rw,rsize=32k,wsize=32k,intr,hard,tcp,addr=192.168.5.83) >>> >>> The /home is mounting on the last one. >>> >>> CPU: 8 Intel(R) Xeon(R) Dual-Core 3.33 Ghz >>> Memory: 114GB RAM >>> HDD Size: 744GB >>> OS: CentOS 4 (64-bits) >>> >>> Thanks for any suggestions, >>> >>> any additional info you need please let me know, >>> >>> Best regards, >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface >> or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
