Hi there is simple fix that I have communicated to a few people with great success on some Linux, Solaris and HP; the problem is with the initialization of DMA/SMA flags when sysinfo gets called.
The following recipe corrects scanf and pre-init problems wih sysinfo - let me know if it works for you. DMA and SMA flags must be pre-initialized before running the build as follows: instructions are for Sage 6.0; this is also a problem on Sage 5.13 and the fix is the same but the directory structure for sage is different (spkg/standard vs upstream for the packages; Sage 3 also removes the patch label - p7 for example) 1 Change to upstream directory were packages used are in compressed (bz2) format 2. You must uncompress atlas-3.10.1.tar.bz2 in <SAGE_ROOT>/upstream/ tar jxvf atlas-3.10.1.tar.bz2 3. cd <SAGE_ROOT>/upstream/atlas-3.10.1/ATLAS/CONFIG/src 4. Edit the file: SpewMakeInc.c around line 720-725 Change the two fprint statements adding the following initial values: from: 720 fprintf(fpout, " SMAFLAGS = "); 721 if (smaflags) 722 fprintf(fpout, " %s", smaflags); 723 fprintf(fpout, "\n DMAFLAGS = "); 724 if (dmaflags) 725 fprintf(fpout, " %s", dmaflags); TO: 720 fprintf(fpout, " SMAFLAGS = -O0"); 721 if (smaflags) 722 fprintf(fpout, " %s", smaflags);upstream/atlas-3.10.1 723 fprintf(fpout, "\n DMAFLAGS = -O0"); 724 if (dmaflags) 725 fprintf(fpout, " %s", dmaflags); 5. Save the filw 6. Move the old compress file to a backup directory (target should be your your temp or backup dir) mv <SAGE_ROOT>/upstream/atlas-3.10.1.tar.bz2 /tmp 7. cd out to: <SAGE_ROOT>/upstream 8. TAR and Recompress the atlas directory you modified above tar cvf atlas-3.10.1.tar atlas-3.10.1 bzip cvf atlas-3.10.1.tar You should now have an atlas-3.10.1.tar.bz2 file in the upstream. 9. cd to <SAGE_ROOT> and re-run the make. This procedure works for standalone ATLAS, Sage-5.13 and Sage-6.0 all these build methods produce the same error. Other thinks to note about ATLAS: - its very finiky on the Assembler version used - Binutils 2.24 (at least 2.22) is recommended - ATLAS will build properly this way with GCC 4.1.x to 4.7.x (all test pass fine) - doing this change does not require you to preset the SAGE_ATLAS_ARCH variable; its best to unset it and let ATLAS optimize or set SAGE_ATLAS_ARCH=fast (newer i3/i5/i7/AMD cpu) or base (older CPU); note a CPU bug affects Sage in this respect - specifying Corei1 will always return Corei2 and standardize to a Corei7 CPU; pre-initializing the flags above avoids this issue as well - this only occurs on some CPU's and OS's but not others and depends upon whether you are running the OS in a VM (VmWare) or not. Thanks, Emanuel Koseos Dept. Comp. Sci. UFV - On Wednesday, January 22, 2014 4:18:18 PM UTC-8, Paul Jones wrote: > > Read in L1 Cache size as = 32KB. >> >> make[8]: Entering directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/tune/sysinfo' >> >> make -j1 RunMulAdd pre=s >> >> make[9]: Entering directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/tune/sysinfo' >> >> /home/paul/sage-6.0/local/bin/gcc -DL2SIZE=4194304 >>> -I/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/include >>> >>> -I/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/../ATLAS//include >>> >>> -I/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/../ATLAS//include/contrib >>> >>> -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_Linux -DATL_ARCH_x86SSE2 >>> -DATL_CPUMHZ=3531 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 >>> -m64 -DATL_FULL_LAPACK -O -fomit-frame-pointer -fPIC -m64 -o xmasrch >>> /home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/../ATLAS//tune/sysinfo/masrch.c >> >> ./xmasrch -p s -o res/sMULADD >> >> xmasrch: >>> /home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/../ATLAS//tune/sysinfo/masrch.c:116: >>> >>> matime: Assertion `fscanf(fp, "%lf", &mflop[i])' failed. >> >> Finding how many mflops required to get .025 second timings: >> >> make[9]: *** [RunMulAdd] Aborted >> >> make[9]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/tune/sysinfo' >> >> make[8]: *** [res/sMULADD] Error 2 >> >> make[8]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/tune/sysinfo' >> >> xsyssum: >>> /home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/../ATLAS//tune/sysinfo/GetSysSum.c:69: >>> >>> getfpinfo0: Assertion `system(fnam) == 0' failed. >> >> make[7]: *** >>> [/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/include/atlas_ssysinfo.h] >>> >>> Aborted >> >> make[7]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/tune/sysinfo' >> >> make[6]: *** >>> [/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/include/atlas_ssysinfo.h] >>> >>> Error 2 >> >> make[6]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/src/auxil' >> >> make[5]: *** [IStage1] Error 2 >> >> make[5]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/bin' >> >> ERROR 621 DURING CACHESIZE SEARCH!!. CHECK INSTALL_LOG/Stage1.log FOR >>> DETAILS. >> >> make[5]: Entering directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/bin' >> >> cd >>> /home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build >>> >>> ; make -j1 error_report >> >> make[6]: Entering directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build' >> >> make -j1 -f Make.top error_report >> >> make[7]: Entering directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build' >> >> uname -a 2>&1 >> bin/INSTALL_LOG/ERROR.LOG >> >> /home/paul/sage-6.0/local/bin/gcc -v 2>&1 >> bin/INSTALL_LOG/ERROR.LOG >> >> Using built-in specs. >> >> COLLECT_GCC=/home/paul/sage-6.0/local/bin/gcc >> >> >>> COLLECT_LTO_WRAPPER=/home/paul/sage-6.0/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.3/lto-wrapper >> >> Target: x86_64-unknown-linux-gnu >> >> Configured with: ../src/configure --prefix=/home/paul/sage-6.0/local >>> --with-local-prefix=/home/paul/sage-6.0/local >>> --with-gmp=/home/paul/sage-6.0/local --with-mpfr=/home/paul/sage-6.0/local >>> --with-mpc=/home/paul/sage-6.0/local --with-system-zlib --disable-multilib >>> --disable-nls >> >> Thread model: posix >> >> gcc version 4.7.3 (GCC) >> >> /home/paul/sage-6.0/local/bin/gcc -V 2>&1 >> bin/INSTALL_LOG/ERROR.LOG >> >> gcc: error: unrecognized command line option '-V' >> >> gcc: fatal error: no input files >> >> compilation terminated. >> >> make[7]: [error_report] Error 1 (ignored) >> >> /home/paul/sage-6.0/local/bin/gcc --version 2>&1 >> >>> bin/INSTALL_LOG/ERROR.LOG >> >> tar cf error_x86SSE264SSE2.tar Make.inc bin/INSTALL_LOG/* >> >> bzip2 error_x86SSE264SSE2.tar >> >> make[7]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build' >> >> make[6]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build' >> >> make[5]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build/bin' >> >> Error report error_<ARCH>.tgz has been created in your top-level ATLAS >> >> directory. Be sure to include this file in any help request. >> >> cat: ../../CONFIG/error.txt: No such file or directory >> >> cat: ../../CONFIG/error.txt: No such file or directory >> >> >>> >>> BEGIN STAGE 1-0-0: SYSTEM PROBE/AUX COMPILE at 15:14 >> >> make[4]: *** [build] Error 255 >> >> make[4]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build' >> >> make[3]: *** [build] Error 2 >> >> make[3]: Leaving directory >>> `/home/paul/sage-6.0/local/var/tmp/sage/build/atlas-3.10.1.p7/src/ATLAS-build' >> >> ------------------------------------------------------------ >> >> File "./spkg-install", line 512, in <module> >> >> assert_success(rc, bad='Failed to build ATLAS.', good='Finished >>> building ATLAS core.') >> >> File "./spkg-install", line 58, in assert_success >> >> traceback.print_stack(file=sys.stdout) >> >> ------------------------------------------------------------ >> >> Error: Failed to build ATLAS. >> >> >>> real 1m37.819s >> >> user 0m33.034s >> >> sys 0m2.253s >> >> ************************************************************************ >> >> Error installing package atlas-3.10.1.p7 >> >> > > I am running a quad core xeon with 8GB of ram with plenty of hard drive > space. I have tried a few things and I am kind of at a loss. Any help you > can provide would be great. Thanks. > -- You received this message because you are subscribed to the Google Groups "sage-support" 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-support. For more options, visit https://groups.google.com/groups/opt_out.
