[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
Hi, I had the same problem a month or two ago with sage 3.1.2 (?) but didn't report it. I had the same problem just now with sage 3.3. I tried fixing the NTL build by removing the -p options but then the build failed for whatever came next (eclib I believe). Then I found this thread and realised it was probably a filesystem issue. I tried doing the sage build on my local drive (/scratch) instead of the NFS drive and now it seems to be working smoothly. david --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
On Sun, Mar 8, 2009 at 8:05 AM, David Harvey dmhar...@cims.nyu.edu wrote: Hi, I had the same problem a month or two ago with sage 3.1.2 (?) but didn't report it. I had the same problem just now with sage 3.3. I tried fixing the NTL build by removing the -p options but then the build failed for whatever came next (eclib I believe). Then I found this thread and realised it was probably a filesystem issue. I tried doing the sage build on my local drive (/scratch) instead of the NFS drive and now it seems to be working smoothly. So it's a NFS drive problem, I am pretty sure about it. Unfortunately that's the only thing available as it seems on our cluster. I'll try to build my customized Sage and just not install the packages that fail, or try to fix them. Ondrej --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
On Wed, Mar 4, 2009 at 9:57 AM, Ondrej Certik ond...@certik.cz wrote: Hi, I tried to build sage on our UNR cluster (not the one with the old g++ that I reported before) and here is what I got: ranlib ntl.a make[2]: Leaving directory `/scratch/ocertik/sage-3.3/spkg/build/ntl-5.4.2.p6/src/src' make[2]: Entering directory `/scratch/ocertik/sage-3.3/spkg/build/ntl-5.4.2.p6/src/src' mkdir -p -m 755 /scratch/ocertik/sage-3.3/local/lib cp -p ntl.a /scratch/ocertik/sage-3.3/local/lib/libntl.a cp: preserving permissions for `/scratch/ocertik/sage-3.3/local/lib/libntl.a': Operation not supported cp: preserving ACL for `/scratch/ocertik/sage-3.3/local/lib/libntl.a': Operation not supported make[2]: *** [install] Error 1 make[2]: Leaving directory `/scratch/ocertik/sage-3.3/spkg/build/ntl-5.4.2.p6/src/src' Failed building install of NTL real 7m0.685s user 5m36.942s sys 0m15.240s sage: An error occurred while installing ntl-5.4.2.p6 So what feature is missing? Seems like cp -p is not working. Install.log attached. If it's something that can be fixed on the cluster, I'll try to report it and get it fixed. Any chance you could build in /tmp instead of /scratch? You could also try changing the spkg-install for NTL to not have the -p and see what happens. William --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
So what feature is missing? Seems like cp -p is not working. Install.log attached. If it's something that can be fixed on the cluster, I'll try to report it and get it fixed. Any chance you could build in /tmp instead of /scratch? You could also try changing the spkg-install for NTL to not have the -p and see what happens. Unfortunately it doesn't allow me to do so --- I need to submit all jobs with qsub and if I try to build in /tmp/, the job fails to run. I now tried to build in my home dir, so let's see what happens. If it fails, I'll try to fix the NTL package. Ondrej --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
On Mar 4, 10:51 am, Ondrej Certik ond...@certik.cz wrote: SNIP Any chance you could build in /tmp instead of /scratch? You could also try changing the spkg-install for NTL to not have the -p and see what happens. Unfortunately it doesn't allow me to do so --- I need to submit all jobs with qsub and if I try to build in /tmp/, the job fails to run. I now tried to build in my home dir, so let's see what happens. If it fails, I'll try to fix the NTL package. * What was the last version of Sage that worked on that box? * What filesystem is scratch? It could be something more exotic since it uses ACLs. * I am afraid that any changes to fix it on your build will just break it somewhere else, so I am more than hesitant to merge anything but absolutely trivial. Ondrej Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
On Wed, Mar 4, 2009 at 9:57 AM, Ondrej Certik ond...@certik.cz wrote: Hi, I tried to build sage on our UNR cluster (not the one with the old g++ that I reported before) and here is what I got: cp -p ntl.a /scratch/ocertik/sage-3.3/local/lib/libntl.a cp: preserving permissions for `/scratch/ocertik/sage-3.3/local/lib/libntl.a': Operation not supported cp: preserving ACL for `/scratch/ocertik/sage-3.3/local/lib/libntl.a': Operation not supported Do you know what kind of filesystem /scratch is? I remember seeing similar error messages (maybe not the exact same error) trying to use cp -p on a thumb drive formatted with Microsoft's FAT filesystem; if /scratch isn't a normal UNIX filesystem, that might be the issue. Carl --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
On Mar 4, 11:27 am, Ondrej Certik ond...@certik.cz wrote: On Wed, Mar 4, 2009 at 2:02 PM, mabshoff mabsh...@googlemail.com wrote: On Mar 4, 10:51 am, Ondrej Certik ond...@certik.cz wrote: SNIP Any chance you could build in /tmp instead of /scratch? You could also try changing the spkg-install for NTL to not have the -p and see what happens. Unfortunately it doesn't allow me to do so --- I need to submit all jobs with qsub and if I try to build in /tmp/, the job fails to run. I now tried to build in my home dir, so let's see what happens. If it fails, I'll try to fix the NTL package. So I tried to build in my home dir and it fails the same. * What was the last version of Sage that worked on that box? I got an account today, so there is no version of sage that is known to work there. ok * What filesystem is scratch? It could be something more exotic since it uses ACLs. mount says: nas-0-0.local:/zpool1/nonvolatile/home/ocertik on /home/ocertik type nfs (rw,tcp,addr=10.255.255.76) nas-0-0.local:/zpool1/volatile/scratch/ocertik on /scratch/ocertik type nfs (rw,tcp,addr=10.255.255.76) Well, I would guess ZFS. so I don't know if there is a way for me to know which filesystem it is. * I am afraid that any changes to fix it on your build will just break it somewhere else, so I am more than hesitant to merge anything but absolutely trivial. Well, I am on my own then. I'll try to fix the NTL, imho there is no reason why it would have to play with permissions. Also, I don't see a reason why Sage couldn't work on the cluster. I thought you had tried to remove the -p from that copy command. Can you try that? Cheers, Michael --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
[sage-devel] Re: sage 3.3 fails to build (preserving permissions problem)
On Wed, Mar 4, 2009 at 2:48 PM, mabshoff mabsh...@googlemail.com wrote: On Mar 4, 11:27 am, Ondrej Certik ond...@certik.cz wrote: On Wed, Mar 4, 2009 at 2:02 PM, mabshoff mabsh...@googlemail.com wrote: On Mar 4, 10:51 am, Ondrej Certik ond...@certik.cz wrote: SNIP Any chance you could build in /tmp instead of /scratch? You could also try changing the spkg-install for NTL to not have the -p and see what happens. Unfortunately it doesn't allow me to do so --- I need to submit all jobs with qsub and if I try to build in /tmp/, the job fails to run. I now tried to build in my home dir, so let's see what happens. If it fails, I'll try to fix the NTL package. So I tried to build in my home dir and it fails the same. * What was the last version of Sage that worked on that box? I got an account today, so there is no version of sage that is known to work there. ok * What filesystem is scratch? It could be something more exotic since it uses ACLs. mount says: nas-0-0.local:/zpool1/nonvolatile/home/ocertik on /home/ocertik type nfs (rw,tcp,addr=10.255.255.76) nas-0-0.local:/zpool1/volatile/scratch/ocertik on /scratch/ocertik type nfs (rw,tcp,addr=10.255.255.76) Well, I would guess ZFS. so I don't know if there is a way for me to know which filesystem it is. * I am afraid that any changes to fix it on your build will just break it somewhere else, so I am more than hesitant to merge anything but absolutely trivial. Well, I am on my own then. I'll try to fix the NTL, imho there is no reason why it would have to play with permissions. Also, I don't see a reason why Sage couldn't work on the cluster. I thought you had tried to remove the -p from that copy command. Can you try that? $ cat /etc/fstab LABEL=/1/ ext3defaults1 1 LABEL=/state/partition /state/partition1 ext3defaults1 2 LABEL=/var /varext3defaults1 2 tmpfs /dev/shmtmpfs defaults0 0 devpts /dev/ptsdevpts gid=5,mode=620 0 0 sysfs /syssysfs defaults0 0 proc/proc procdefaults0 0 LABEL=SWAP-sda3 swapswapdefaults0 0 Yep, I'll do that, but probably in few days, as the net connection here is really bad and I need to work on other things now. Ondrej --~--~-~--~~~---~--~~ To post to this group, send email to sage-devel@googlegroups.com To unsubscribe from this group, send email to sage-devel-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sage-devel URLs: http://www.sagemath.org -~--~~~~--~~--~--~---
