On Thu, Mar 14, 2019 at 5:44 PM Ai Bo <[email protected]> wrote: > > I see. Thank you. > As I don't know how and when the files will be cleaned on the local disk and > I don't know when my program, if launched at local disk, will be killed.
A typical HPC center policy with scratch disks is that files live a certain amount of time, i.e. most probably 1 month since creation. Surely local disks are not cleaned at random moments, otherwise what's point of having them, they are basically useless. > > I downloaded the binary package. I am a little bit confused. Does the binary > package know where I already build ./sage? I think you need to start from the beginning, again. But I think it's much better idea to use the local disks, surely 30 days is long enough for a lot of work, and then you wipe your local disk, copy there files from NFS, and may start again. > > On Thu, Mar 14, 2019 at 12:51 AM Dima Pasechnik <[email protected]> wrote: >> >> On Thu, Mar 14, 2019 at 7:24 AM Dima Pasechnik <[email protected]> wrote: >> > >> > On Thu, Mar 14, 2019 at 7:09 AM Dima Pasechnik <[email protected]> wrote: >> > > >> > > On Thu, Mar 14, 2019 at 3:39 AM Ai Bo <[email protected]> wrote: >> > > > >> > > > Sorry, it doesn't work if I build on local disk and then copy to /nfs. >> > > > I got error: >> > > > bash-4.3$ ./sage >> > >> > But did you try moving it back to the local disk, before starting it? >> > Indeed, you just need to have a copy of your files on NFS, and copy it >> > to the local disk for running. >> (It's important that it's moved to the same place in the directory >> tree where it was built). >> > >> > Sorry for confusion, again. >> > >> > > > >> > > > ERROR: The Sage installation tree has moved >> > > > >> > > > from /tmp/.../sage-8.6 >> > > > to /nfs/.../Sage/sage-8.6 >> > > > >> > > > This is not supported, and Sage will not work. To install Sage from a >> > > > binary package: >> > > >> > > yes, you need to create a binary package in this case. It (not the >> > > unpacked result, but the package itsel) can be >> > > moved. Indeed, Sage binary installers have to come from somewhere, >> > > right? See >> > > >> > > https://github.com/sagemath/binary-pkg >> > > >> > > Sorry, I should have mentioned this earlier. It has to be built from >> > > scratch, AFAIK. >> > > >> > > >> > > > >> > > > As I mentioned before, I can't save files on local disk more then 30 >> > > > days. But it seems I can't copy the whole directory to /nfs either. >> > > > >> > > > Please advise. >> > > > >> > > > On Wed, Mar 13, 2019 at 11:21 AM Ai Bo <[email protected]> wrote: >> > > >> >> > > >> I see. Will try. Thank you. >> > > >> >> > > >> On Wed, Mar 13, 2019 at 11:04 AM Dima Pasechnik <[email protected]> >> > > >> wrote: >> > > >>> >> > > >>> On Wed, Mar 13, 2019 at 5:57 PM Ai Bo <[email protected]> wrote: >> > > >>> > >> > > >>> > Sorry, I can't. All local disks are cleaned out every 30 days. >> > > >>> >> > > >>> but building does not take that long. :-) >> > > >>> Besides, once you have a working build you can, with a bit of >> > > >>> effort, move it >> > > >>> around. >> > > >>> >> > > >>> > >> > > >>> > On Wed, Mar 13, 2019 at 9:43 AM Dima Pasechnik <[email protected]> >> > > >>> > wrote: >> > > >>> >> >> > > >>> >> On Wed, Mar 13, 2019 at 4:18 PM Ai Bo <[email protected]> wrote: >> > > >>> >> > >> > > >>> >> > Yes. This is done on NFS. >> > > >>> >> > I can't build on local disks as this is not on a particular >> > > >>> >> > machine. But I do own my own NFS disks. >> > > >>> >> >> > > >>> >> Normally multi-user systems have a "scratch" partition, a local >> > > >>> >> disk >> > > >>> >> reserved for this kind of jobs, which is not backed up, but is >> > > >>> >> fast to >> > > >>> >> access (as opposed to NFS). >> > > >>> >> Ask your system admins for access to such a partition, it's a >> > > >>> >> perfectly reasonable request. >> > > >>> >> >> > > >>> >> > Also, the reason I want to build on my machine as when I use >> > > >>> >> > the online version(server), a long running program will be >> > > >>> >> > paused from time to time. I want to run on some machines I have >> > > >>> >> > access to instead. >> > > >>> >> > >> > > >>> >> > If I can't build on NFS, this seems to be a dead end too. >> > > >>> >> > >> > > >>> >> > On Wed, Mar 13, 2019 at 9:03 AM E. Madison Bray >> > > >>> >> > <[email protected]> wrote: >> > > >>> >> >> >> > > >>> >> >> On Wed, Mar 13, 2019 at 4:58 PM Dima Pasechnik >> > > >>> >> >> <[email protected]> wrote: >> > > >>> >> >> > >> > > >>> >> >> > By looking at the output it looks as if the build it on an >> > > >>> >> >> > NFS, and this is known to be severely broken. Could you do >> > > >>> >> >> > the build on a local disk? >> > > >>> >> >> >> > > >>> >> >> Oh, nice catch. Yes, many build tools can have problems on >> > > >>> >> >> NFS, >> > > >>> >> >> especially on older kernels. For example if timestamps are not >> > > >>> >> >> fine-grained enough you can end up with screwy issues where >> > > >>> >> >> some >> > > >>> >> >> dependencies don't get rebuilt properly and things like that. >> > > >>> >> >> >> > > >>> >> >> > On Wed, 13 Mar 2019 15:44 E. Madison Bray, >> > > >>> >> >> > <[email protected]> wrote: >> > > >>> >> >> >> >> > > >>> >> >> >> On Wed, Mar 13, 2019 at 4:40 AM Ai Bo <[email protected]> >> > > >>> >> >> >> wrote: >> > > >>> >> >> >> > >> > > >>> >> >> >> > Just compiled sage from source code on Linux. >> > > >>> >> >> >> > When I launched ./sage, I can do simple math like 2+2 >> > > >>> >> >> >> > which give correct >> > > >>> >> >> >> > But when I type: >> > > >>> >> >> >> > sage: import sage.graphs >> > > >>> >> >> >> > >> > > >>> >> >> >> > sage: print("%d" % len(list(graphs.nauty_geng("8")))) >> > > >>> >> >> >> > >> > > >>> >> >> >> > sage: print("%d" % len(list(graphs(8)))) >> > > >>> >> >> >> > >> > > >>> >> >> >> > I got 0 for both which are not as expected. Something is >> > > >>> >> >> >> > wrong. Please help. >> > > >>> >> >> >> >> > > >>> >> >> >> I think that, considering the problems you've mentioned in >> > > >>> >> >> >> other >> > > >>> >> >> >> threads, you probably have a severely broken build. Did >> > > >>> >> >> >> you take my >> > > >>> >> >> >> previous advice of running >> > > >>> >> >> >> >> > > >>> >> >> >> $ make distclean >> > > >>> >> >> >> >> > > >>> >> >> >> and starting over again, making sure you can complete the >> > > >>> >> >> >> full build >> > > >>> >> >> >> without errors? >> > > >>> >> >> >> >> > > >>> >> >> >> Also, is there a specific reason you need to build Sage >> > > >>> >> >> >> yourself on >> > > >>> >> >> >> this specific machine? Not that I doubt it, nor that I >> > > >>> >> >> >> wouldn't like >> > > >>> >> >> >> to try to help, but it seems like a lot of effort and >> > > >>> >> >> >> frustration for >> > > >>> >> >> >> dubious benefit. >> > > >>> >> >> >> >> > > >>> >> >> >> Could you mention again exactly which Linux distribution >> > > >>> >> >> >> this is, and >> > > >>> >> >> >> on what CPU architecture? Perhaps I can start up a VM and >> > > >>> >> >> >> try to >> > > >>> >> >> >> build Sage myself to see if there are any specific problems >> > > >>> >> >> >> I can >> > > >>> >> >> >> identify. >> > > >>> >> >> >> >> > > >>> >> >> >> -- >> > > >>> >> >> >> You received this message because you are subscribed to the >> > > >>> >> >> >> Google Groups "sage-devel" group. >> > > >>> >> >> >> To unsubscribe from this group and stop receiving emails >> > > >>> >> >> >> from it, send an email to >> > > >>> >> >> >> [email protected]. >> > > >>> >> >> >> To post to this group, send email to >> > > >>> >> >> >> [email protected]. >> > > >>> >> >> >> Visit this group at >> > > >>> >> >> >> https://groups.google.com/group/sage-devel. >> > > >>> >> >> >> For more options, visit https://groups.google.com/d/optout. >> > > >>> >> >> > >> > > >>> >> >> > -- >> > > >>> >> >> > You received this message because you are subscribed to the >> > > >>> >> >> > Google Groups "sage-devel" group. >> > > >>> >> 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