Can you try out http://trac.sagemath.org/17349 instead? This should always link in atlas, regardless of X11. If anything this should give us consistent behavior.
On Saturday, November 22, 2014 12:47:27 PM UTC, pipedream wrote: > > Hi > > I think I'm getting this the wrong way around. Is it not that > > snapperkob build fails where there is NO system ATLAS installed, so it is > using SAGE ATLAS. > > muizenberg works, where libatlas3-base is installed. > > How does a fix to NOT use the system ATLAS help, if the system ATLAS was > not present on snapperkob? > > libx11-dev is installed on both. > > I am installaing libatlas3-base on snapperkob to try again. > > Note there is now load shedding in South Africa, and for the next three > nights at 8pm South Africa time I expect snapperkob to be down for 2.5 > hours. I hope this build finishes before that. > > Regards, > Jan > > > On 22 November 2014 01:09, Volker Braun <vbrau...@gmail.com <javascript:>> > wrote: > >> I've added a commit to always use our ATLAS to >> http://trac.sagemath.org/ticket/17349, if nothing else then this will >> let us debug the issue in a sane way... >> >> >> On Friday, November 21, 2014 10:24:22 PM UTC, Volker Braun wrote: >>> >>> R only uses our ATLAS if X development stuff is installed. The whole >>> logic in the spkg-install is suspicious... >>> >>> >>> >>> >>> On Friday, November 21, 2014 7:02:52 PM UTC, pipedream wrote: >>>> >>>> Hi >>>> >>>> I didn't set SAGE_FAT_BINARY on either. >>>> >>>> Actually, I have atlas on muizenberg not snapperkob: >>>> >>>> 0 root@muizenberg:~#dpkg -l |grep atlas >>>> ii libatlas3-base >>>> 3.10.1-4 amd64 >>>> Automatically Tuned Linear Algebra Software, generic shared >>>> 0 root@muizenberg:~# >>>> >>>> >>>> 1 jan@snapperkob:~/sage-6.4$dpkg -l |grep atlas >>>> 1 jan@snapperkob:~/sage-6.4$ >>>> >>>> >>>> Regards, >>>> Jan >>>> >>>> On 21 November 2014 14:54, Volker Braun <vbrau...@gmail.com> wrote: >>>> >>>>> You didn't set SAGE_FAT_BINARY=yes I guess since in that case we >>>>> configure R --without-ICU >>>>> >>>>> I take it you have Ubuntu's version of ATLAS installed on snapperkob >>>>> and not on muizenberg? >>>>> >>>>> >>>>> >>>>> On Friday, November 21, 2014 8:21:28 AM UTC, pipedream wrote: >>>>> >>>>>> Hi Volker, >>>>>> >>>>>> I repeated on snapperkob, not via buildbot just as my own user: >>>>>> >>>>>> real 125m41.153s >>>>>> user 208m24.169s >>>>>> sys 20m6.421s >>>>>> *************************************************************** >>>>>> Error building Sage. >>>>>> >>>>>> The following package(s) may have failed to build: >>>>>> >>>>>> package: r-3.1.1.p0 >>>>>> log file: /home/jan/sage-6.4/logs/pkgs/r-3.1.1.p0.log >>>>>> build directory: /home/jan/sage-6.4/local/var/t >>>>>> mp/sage/build/r-3.1.1.p0 >>>>>> >>>>>> The build directory may contain configuration files and other >>>>>> potentially >>>>>> helpful information. WARNING: if you now run 'make' again, the build >>>>>> directory will, by default, be deleted. Set the environment variable >>>>>> SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. >>>>>> >>>>>> make: *** [build] Error 1 >>>>>> 2 jan@snapperkob:~/sage-6.4$ >>>>>> >>>>>> I can try investigate what is different on muizenberg and snapperkob >>>>>> or my user on muizenberg & snapperkob. >>>>>> >>>>>> They are both Dell Optiplex, 64 bit, entirely up to date Ubuntu >>>>>> 14.04.1, though: >>>>>> >>>>>> snapperkob is a text-only server install >>>>>> muizenberg is a GUI full desktop install >>>>>> >>>>>> There is little difference underneath in ubuntu though. It is the >>>>>> same kernel. (the package linux-server depends on linux-generic which is >>>>>> also on the desktop, and depends on the actual kernel) >>>>>> >>>>>> They both have the Intel E8400 CPU. They both have 8G RAM. >>>>>> >>>>>> Comparing the logs for the two R builds, I found these differences in >>>>>> the configure parts, due to different packages available on the system: >>>>>> >>>>>> muizenberg (built successfully) >>>>>> >>>>>> R is now configured for x86_64-unknown-linux-gnu >>>>>> >>>>>> Source directory: . >>>>>> Installation directory: /srv/sysadm/sage/sage-6.4/local >>>>>> >>>>>> C compiler: gcc -std=gnu99 -g -O2 >>>>>> Fortran 77 compiler: gfortran -g -O2 >>>>>> >>>>>> C++ compiler: g++ >>>>>> C++ 11 compiler: g++ -std=c++11 >>>>>> Fortran 90/95 compiler: gfortran -g -O2 >>>>>> Obj-C compiler: >>>>>> >>>>>> Interfaces supported: >>>>>> External libraries: readline, ICU, lzma >>>>>> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >>>>>> Options enabled: shared R library, shared BLAS, R >>>>>> profiling >>>>>> >>>>>> Recommended packages: yes >>>>>> >>>>>> >>>>>> And snapperkob (failed): >>>>>> >>>>>> R is now configured for x86_64-unknown-linux-gnu >>>>>> >>>>>> Source directory: . >>>>>> Installation directory: /home/jan/sage-6.4/local >>>>>> >>>>>> C compiler: gcc -std=gnu99 -g -O2 >>>>>> Fortran 77 compiler: gfortran -g -O2 >>>>>> >>>>>> C++ compiler: g++ >>>>>> C++ 11 compiler: g++ -std=c++11 >>>>>> Fortran 90/95 compiler: gfortran -g -O2 >>>>>> Obj-C compiler: >>>>>> >>>>>> Interfaces supported: X11, tcltk >>>>>> External libraries: readline, BLAS(ATLAS), LAPACK(generic), >>>>>> ICU >>>>>> Additional capabilities: PNG, JPEG, NLS, cairo >>>>>> Options enabled: shared R library, R profiling >>>>>> >>>>>> Recommended packages: yes >>>>>> >>>>>> >>>>>> Can you think what I can change on snapperkob to test? BLAS or LAPACK >>>>>> perhaps? >>>>>> >>>>>> Regards, >>>>>> Jan >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 20 November 2014 20:35, Jan Groenewald <j...@aims.ac.za> wrote: >>>>>> >>>>>>> Different machine: >>>>>>> >>>>>>> 0 root@muizenberg:/srv/sysadm/sage#dpkg -S >>>>>>> /usr/lib/x86_64-linux-gnu/libgomp.so.* >>>>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >>>>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >>>>>>> 0 root@muizenberg:/srv/sysadm/sage#dpkg -l libgomp1 >>>>>>> Desired=Unknown/Install/Remove/Purge/Hold >>>>>>> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig >>>>>>> -aWait/Trig-pend >>>>>>> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) >>>>>>> ||/ Name >>>>>>> Version Architecture Description >>>>>>> +++-=======================================-================ >>>>>>> ========-========================-========================== >>>>>>> ========================================================= >>>>>>> ii libgomp1:amd64 >>>>>>> 4.8.2-19ubuntu1 amd64 GCC OpenMP (GOMP) >>>>>>> support >>>>>>> library >>>>>>> 0 root@muizenberg:/srv/sysadm/sage# >>>>>>> >>>>>>> Same version: >>>>>>> >>>>>>> 0 jan@snapperkob:~/src$dpkg -S /usr/lib/x86_64-linux-gnu/libg >>>>>>> omp.so.* >>>>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >>>>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >>>>>>> 0 jan@snapperkob:~/src$dpkg -l libgomp1 >>>>>>> Desired=Unknown/Install/Remove/Purge/Hold >>>>>>> | Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig >>>>>>> -aWait/Trig-pend >>>>>>> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) >>>>>>> ||/ Name >>>>>>> Version Architecture Description >>>>>>> +++-=======================================-================ >>>>>>> ========-========================-========================== >>>>>>> ========================================================= >>>>>>> ii libgomp1:amd64 >>>>>>> 4.8.2-19ubuntu1 amd64 GCC OpenMP (GOMP) >>>>>>> support >>>>>>> library >>>>>>> 0 jan@snapperkob:~/src$ >>>>>>> >>>>>>> Regards, >>>>>>> Jan >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 20 November 2014 18:32, Volker Braun <vbrau...@gmail.com> wrote: >>>>>>> >>>>>>>> Is this on "snapperkob" or on a different machine? Do you >>>>>>>> have /usr/lib/x86_64-linux-gnu/libgomp.so.* and if yes, which >>>>>>>> version? >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thursday, November 20, 2014 12:02:18 PM UTC, pipedream wrote: >>>>>>>>> >>>>>>>>> Hi >>>>>>>>> >>>>>>>>> I rebuilt sage from a cleanly unpacked source tree on Ubuntu >>>>>>>>> 14.04, and it still did not fail on R >>>>>>>>> >>>>>>>>> >>>>>>>>> export SAGE_INSTALL_GCC=yes >>>>>>>>> make >>>>>>>>> ... >>>>>>>>> Successfully installed r-3.1.1.p0 >>>>>>>>> >>>>>>>>> I'd like to assist running any tests to get this fixed. >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Jan >>>>>>>>> >>>>>>>>> >>>>>>>>> On 19 November 2014 09:09, Jan Groenewald <j...@aims.ac.za> wrote: >>>>>>>>> >>>>>>>>>> Hi >>>>>>>>>> >>>>>>>>>> I did >>>>>>>>>> >>>>>>>>>> $SAGE_INSTALL_GCC=yes make >>>>>>>>>> >>>>>>>>>> in the already built source tree, and it seemed to rebuild the >>>>>>>>>> relevant parts without failing. Is that enough or should I try it in >>>>>>>>>> a >>>>>>>>>> cleanly unpacked source tree? >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Jan >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On 18 November 2014 15:56, Jan Groenewald <j...@aims.ac.za> >>>>>>>>>> wrote: >>>>>>>>>> >>>>>>>>>>> Will do. >>>>>>>>>>> >>>>>>>>>>> Regards, >>>>>>>>>>> Jan >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On 18 November 2014 15:29, Volker Braun <vbrau...@gmail.com> >>>>>>>>>>> wrote: >>>>>>>>>>> >>>>>>>>>>>> Try building with SAGE_INSTALL_GCC=yes, I'm pretty sure this is >>>>>>>>>>>> causing the problem. >>>>>>>>>>>> >>>>>>>>>>>> On Tuesday, November 18, 2014 11:56:03 AM UTC, pipedream wrote: >>>>>>>>>>>>> >>>>>>>>>>>>> Hi >>>>>>>>>>>>> >>>>>>>>>>>>> This is strange, the error I see is: >>>>>>>>>>>>> >>>>>>>>>>>>> /home/buildbot/build/sage/snapperkob/sage_git/build/local/var/tmp/sage/build/r-3.1.1.p0/src/bin/exec/R: >>>>>>>>>>>>> /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not >>>>>>>>>>>>> found (required by >>>>>>>>>>>>> /home/buildbot/build/sage/snapperkob/sage_git/build/local/var/tmp/sage/build/r-3.1.1.p0/src/lib/libR.so) >>>>>>>>>>>>> >>>>>>>>>>>>> I have the same version of libgomp1 (4.8.2-19ubuntu1) >>>>>>>>>>>>> installed on my 14.04 64bit desktop as that builder (snapperkob) >>>>>>>>>>>>> and yet >>>>>>>>>>>>> sage 6.4 built succesfully on my desktop yesterday: >>>>>>>>>>>>> >>>>>>>>>>>>> "Successfully installed r-3.1.1.p0" >>>>>>>>>>>>> >>>>>>>>>>>>> Regards, >>>>>>>>>>>>> Jan >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On 18 November 2014 13:22, Volker Braun <vbrau...@gmail.com> >>>>>>>>>>>>> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> The build failed because R insists on using openmp for some >>>>>>>>>>>>>> reason, but the openmp libraries are not installed (or of the >>>>>>>>>>>>>> wrong >>>>>>>>>>>>>> version): >>>>>>>>>>>>>> >>>>>>>>>>>>>> http://build.sagedev.org/release/builders/Zbin%20%20fast%20A >>>>>>>>>>>>>> IMS%20snapperkob%20%28Ubuntu%2014.04%20x86_64%29%20binary/bu >>>>>>>>>>>>>> ilds/1/steps/compile_2/logs/r-project >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Tuesday, November 18, 2014 5:00:26 AM UTC, pipedream wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Hi >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> I do not see the 14.04 Ubuntu binaries here. >>>>>>>>>>>>>>> http://boxen.math.washington.edu/home/sagemath/sage-mirror/l >>>>>>>>>>>>>>> inux/64bit/index.html >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Are they not automatically generated? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Regards, >>>>>>>>>>>>>>> Jan >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On 17 November 2014 17:17, kcrisman <kcri...@gmail.com> >>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> The release notes have a broken link in them: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> http://boxen.math.washington. >>>>>>>>>>>>>>>>> edu/home/release/sage-6.4/tickets.html >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Yes, that has been reported before... >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> By the way, Jeroen, I think I finished all the changes I'm >>>>>>>>>>>>>>>> going to for now. Long-term, it would be fun to do some >>>>>>>>>>>>>>>> database thingie >>>>>>>>>>>>>>>> to standardize names of a few very frequent contributors who >>>>>>>>>>>>>>>> have them in a >>>>>>>>>>>>>>>> couple different formats. >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>> -- >>>>>>>>> .~. >>>>>>>>> /V\ Jan Groenewald >>>>>>>>> /( )\ www.aims.ac.za >>>>>>>>> ^^-^^ >>>>>>>>> >>>>>>>> -- >>>>>>>> You received this message because you are subscribed to the Google >>>>>>>> Groups "sage-release" group. >>>>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>>>> send an email to sage-release...@googlegroups.com. >>>>>>>> To post to this group, send email to sage-r...@googlegroups.com. >>>>>>>> Visit this group at http://groups.google.com/group/sage-release. >>>>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> .~. >>>>>>> /V\ Jan Groenewald >>>>>>> /( )\ www.aims.ac.za >>>>>>> ^^-^^ >>>>>>> >>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> .~. >>>>>> /V\ Jan Groenewald >>>>>> /( )\ www.aims.ac.za >>>>>> ^^-^^ >>>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "sage-release" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to sage-release...@googlegroups.com. >>>>> To post to this group, send email to sage-r...@googlegroups.com. >>>>> Visit this group at http://groups.google.com/group/sage-release. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>> >>>> >>>> >>>> -- >>>> .~. >>>> /V\ Jan Groenewald >>>> /( )\ www.aims.ac.za >>>> ^^-^^ >>>> >>> -- >> You received this message because you are subscribed to the Google Groups >> "sage-release" group. >> To unsubscribe from this group and stop receiving emails from it, send an >> email to sage-release...@googlegroups.com <javascript:>. >> To post to this group, send email to sage-r...@googlegroups.com >> <javascript:>. >> Visit this group at http://groups.google.com/group/sage-release. >> For more options, visit https://groups.google.com/d/optout. >> > > > > -- > .~. > /V\ Jan Groenewald > /( )\ www.aims.ac.za > ^^-^^ > -- You received this message because you are subscribed to the Google Groups "sage-release" group. To unsubscribe from this group and stop receiving emails from it, send an email to sage-release+unsubscr...@googlegroups.com. To post to this group, send email to sage-release@googlegroups.com. Visit this group at http://groups.google.com/group/sage-release. For more options, visit https://groups.google.com/d/optout.
