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 <[email protected]> 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/tmp/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 <[email protected]> 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$dpkg -S /usr/lib/x86_64-linux-gnu/libgomp.so.* >>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >>>>> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >>>>> 0 jan@snapperkob:~/src$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 <[email protected]> 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 <[email protected]> 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 <[email protected]> wrote: >>>>>>>> >>>>>>>>> Will do. >>>>>>>>> >>>>>>>>> Regards, >>>>>>>>> Jan >>>>>>>>> >>>>>>>>> >>>>>>>>> On 18 November 2014 15:29, Volker Braun <[email protected]> >>>>>>>>> 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 <[email protected]> >>>>>>>>>>> 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/ >>>>>>>>>>>> builds/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 <[email protected]> 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 [email protected]. >>>>>> To post to this group, send email to [email protected]. >>>>>> 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 [email protected]. >>> To post to this group, send email to [email protected]. >>> 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 [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/sage-release. For more options, visit https://groups.google.com/d/optout.
