Description of problem: octave crash calling the eig function on older AMD CPUs Version-Release number of selected component (if applicable): atlas-3.8.3-12.fc12.x86_64 octave-3.2.3-4.fc12.x86_64 How reproducible: 100% Steps to Reproduce: 1. open Octave and run 2.octave:1> a=diag([1:72]); eig(a) Actual results: panic: Illegal instruction -- stopping myself... attempting to save variables to `octave-core'... save to `octave-core' complete Illegal instruction (core dumped) Expected results: A vector of integers from 1 to 72 Additional info: https://bugzilla.redhat.com/show_bug.cgi?id=573074 https://www-old.cae.wisc.edu/pipermail/bug-octave/2010-March/010555.html
A similar error message occurs if you do the following: octave:1> a=rand(3); octave:2> save A octave:3> clear octave:4> load A panic: Segmentation fault -- stopping myself... attempting to save variables to `octave-core'... save to `octave-core' complete Segmentation fault (core dumped) This is on octave-3.2.3-4.fc12.x86_64
I just checked and the above error also occurs with the version: octave-3.2.3-4.fc12.i686 These errors are occurring on Intel CPU's, not AMD as the original poster noted.
This is a completely different problem. BTW, you do realise that a and A are different variables in octave. save A actually saves entire octave work space into file named A. If you want just to save variable "a" you need to do something like save a.txt a (that saves the matrix "a" into file "a.txt").
The intent was to save the entire work space. However, whether I say "save A" or "save a", the segmentation fault still occurs when you clear than issue the load command.
The problem appears to be due to some octave-forge package. At least if I uninstall octave-forge (or start octave as octave -f) it seems to be working fine.
I think it is problem with package "ann". As a quick fix you can remove /usr/share/octave/packages/ann* directory. I will file a separate bug report for this.
(In reply to comment #6) > I think it is problem with package "ann". As a quick fix you can > remove /usr/share/octave/packages/ann* directory. > > I will file a separate bug report for this. Should this bug then be closed as a dupe of bug #562276?
I think the original bug report is still (?) valid. The comment by Ed Friedman diverted it to a dupe of #562276. Dmitri. --
I guess we should request info from the submitter if the problem still exist with the current version of ATLAS. The problem seems to affect only some specific CPUs so it is hard to reproduce elsewhere. Dmitri. --
(In reply to comment #9) > I guess we should request info from the submitter if the problem still > exist with the current version of ATLAS. The problem seems to affect only > some specific CPUs so it is hard to reproduce elsewhere. Andy: does this problem still exist? Ideally test in F-13 if you have installed as well, to see if it's different between F-12 and F-13.
Still a problem in the latest Fedora 12: uname -a Linux opt 2.6.32.16-141.fc12.x86_64 #1 SMP Wed Jul 7 04:49:59 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux rpm -q octave atlas octave-3.2.3-4.fc12.x86_64 atlas-3.8.3-12.fc12.x86_64 cat /proc/cpuinfo processor : 0 vendor_id : AuthenticAMD cpu family : 15 model : 5 model name : AMD Opteron(tm) Processor 250 stepping : 10 cpu MHz : 2405.882 cache size : 1024 KB fpu : yes fpu_exception : yes cpuid level : 1 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow rep_good extd_apicid bogomips : 4811.76 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 40 bits physical, 48 bits virtual power management: ts fid vid ttp processor : 1 vendor_id : AuthenticAMD cpu family : 15 model : 5 model name : AMD Opteron(tm) Processor 250 stepping : 10 cpu MHz : 2405.882 cache size : 1024 KB fpu : yes fpu_exception : yes cpuid level : 1 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow rep_good extd_apicid bogomips : 4810.07 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 40 bits physical, 48 bits virtual power management: ts fid vid ttp octave octave:1> [Veig D] = eig(full(diag([1:200]))); panic: Illegal instruction -- stopping myself... attempting to save variables to `octave-core'... save to `octave-core' complete Illegal instruction (core dumped)
A different AMD, Fedora 12: uname -a Linux math.ucdenver.edu 2.6.32.14-127.fc12.x86_64 #1 SMP Fri May 28 04:30:39 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux rpm -q octave atlas octave-3.2.3-4.fc12.x86_64 atlas-3.8.3-12.fc12.x86_64 cat /proc/cpuinfo processor : 0 vendor_id : AuthenticAMD cpu family : 15 model : 5 model name : AMD Opteron(tm) Processor 248 stepping : 8 cpu MHz : 2192.786 cache size : 1024 KB fpu : yes fpu_exception : yes cpuid level : 1 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow rep_good bogomips : 4385.57 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 40 bits physical, 48 bits virtual power management: ts ttp processor : 1 vendor_id : AuthenticAMD cpu family : 15 model : 5 model name : AMD Opteron(tm) Processor 248 stepping : 8 cpu MHz : 2192.786 cache size : 1024 KB fpu : yes fpu_exception : yes cpuid level : 1 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 syscall nx mmxext lm 3dnowext 3dnow rep_good bogomips : 4384.95 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 40 bits physical, 48 bits virtual power management: ts ttp octave octave:1> [Veig D] = eig(full(diag([1:200]))); panic: Illegal instruction -- stopping myself... attempting to save variables to `octave-core'... save to `octave-core' complete Illegal instruction
Can you retest on F-13? It does appear to be AMD-specific. It would be nice if the maintainer could chime in on this bug. I can't reproduce on F-13 with these packages. # rpm -q octave octave-forge atlas octave-3.2.4-2.fc13.x86_64 octave-forge-20090607-17.fc13.x86_64 atlas-3.8.3-15.fc13.x86_64 # octave GNU Octave, version 3.2.4 Copyright (C) 2009 John W. Eaton and others. This is free software; see the source code for copying conditions. There is ABSOLUTELY NO WARRANTY; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. For details, type `warranty'. Octave was configured for "x86_64-redhat-linux-gnu". Additional information about Octave is available at http://www.octave.org. Please contribute if you find this software useful. For more information, visit http://www.octave.org/help-wanted.html Report bugs to <bug> (but first, please read http://www.octave.org/bugs.html to learn how to write a helpful report). For information about changes from previous versions, type `news'. warning: mark_as_command is obsolete and will be removed from a future version of Octave octave:1> [Veig D] = eig(full(diag([1:200]))); octave:2> cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 23 model name : Intel(R) Core(TM)2 Duo CPU E8500 @ 3.16GHz stepping : 6 cpu MHz : 2000.000 cache size : 6144 KB physical id : 0 siblings : 2 core id : 0 cpu cores : 2 apicid : 0 initial apicid : 0 fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx lm constant_tsc arch_perfmon pebs bts rep_good aperfmperf pni dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm sse4_1 lahf_lm tpr_shadow vnmi flexpriority bogomips : 6317.50 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management:
I'll try for a fix over the weekend. Thanks for your patience.
I'll fix the package to build a sse2 subpackage on the x86_64 arch too. Please test the scratch builds in the links below and let me know if works for you. Thanks. F-13: http://koji.fedoraproject.org/koji/taskinfo?taskID=2350161 F-12: http://koji.fedoraproject.org/koji/taskinfo?taskID=2350226
I have tested this on on Linux opt 2.6.32.16-141.fc12.x86_64 #1 SMP Wed Jul 7 04:49:59 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux see above for more system info. I've gotten http://koji.fedoraproject.org/koji/getfile?taskID=2350226&name=atlas-3.8.3-16.fc12.x86_64.rpm and installed by rpm -ivh --force atlas-3.8.3-16.fc12.x86_64.rpm since rpm -ivh atlas-3.8.3-16.fc12.x86_64.rpm Preparing... ########################################### [100%] file /usr/lib64/atlas/libatlas.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 file /usr/lib64/atlas/libcblas.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 file /usr/lib64/atlas/libclapack.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 file /usr/lib64/atlas/libf77blas.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 file /usr/lib64/atlas/liblapack.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 file /usr/lib64/atlas/libptcblas.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 file /usr/lib64/atlas/libptf77blas.so.3.0 from install of atlas-3.8.3-16.fc12.x86_64 conflicts with file from package atlas-3.8.3-12.fc12.x86_64 I could not erase the previous version since pm -e atlas-3.8.3-12.fc12.x86_64 error: Failed dependencies: libatlas.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 libatlas.so.3()(64bit) is needed by (installed) octave-forge-20090607-17.fc12.x86_64 libcblas.so.3()(64bit) is needed by (installed) suitesparse-3.4.0-2.fc12.x86_64 libf77blas.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 libf77blas.so.3()(64bit) is needed by (installed) octave-forge-20090607-17.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) arpack-2.1-12.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) suitesparse-3.4.0-2.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) qrupdate-1.1.1-1.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) octave-forge-20090607-17.fc12.x86_64 So now I have rpm -q octave atlas octave-3.2.3-4.fc12.x86_64 atlas-3.8.3-12.fc12.x86_64 atlas-3.8.3-16.fc12.x86_64 This does not fix it. Still the same error octave [Veig D] = eig(full(diag([1:200]))); panic: Illegal instruction -- stopping myself... attempting to save variables to `octave-core'... save to `octave-core' complete Illegal instruction (core dumped) But octave still probably uses atlas-3.8.3-12. Perhaps my installation is not good. I am just a regular user, so please help me to install it properly so that I could test it.
(In reply to comment #16) > > So now I have > > rpm -q octave atlas > octave-3.2.3-4.fc12.x86_64 > atlas-3.8.3-12.fc12.x86_64 > atlas-3.8.3-16.fc12.x86_64 > The above is not good, and what you really need is the atlas-sse2 subpackage. So you need to remove both atlas installations you have now; run 'rpm -e atlas-3.8.3-12.fc12.x86_64 atlas-3.8.3-16.fc12.x86_64'. and then install the new atlas-sse2 package; 'rpm -ivh http://koji.fedoraproject.org/koji/getfile?taskID=2350226&name=atlas-sse2-3.8.3-16.fc12.x86_64.rpm'.
As I have already written in the previous post, rpm -e atlas-3.8.3-12.fc12.x86_64 error: Failed dependencies: libatlas.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 libatlas.so.3()(64bit) is needed by (installed) octave-forge-20090607-17.fc12.x86_64 libcblas.so.3()(64bit) is needed by (installed) suitesparse-3.4.0-2.fc12.x86_64 libf77blas.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 libf77blas.so.3()(64bit) is needed by (installed) octave-forge-20090607-17.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) arpack-2.1-12.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) suitesparse-3.4.0-2.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) qrupdate-1.1.1-1.fc12.x86_64 liblapack.so.3()(64bit) is needed by (installed) octave-forge-20090607-17.fc12.x86_64 How do I remove it?
(In reply to comment #18) > As I have already written in the previous post, > > rpm -e atlas-3.8.3-12.fc12.x86_64 > error: Failed dependencies: > libatlas.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 > libatlas.so.3()(64bit) is needed by (installed) > octave-forge-20090607-17.fc12.x86_64 > libcblas.so.3()(64bit) is needed by (installed) > suitesparse-3.4.0-2.fc12.x86_64 > libf77blas.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 > libf77blas.so.3()(64bit) is needed by (installed) > octave-forge-20090607-17.fc12.x86_64 > liblapack.so.3()(64bit) is needed by (installed) arpack-2.1-12.fc12.x86_64 > liblapack.so.3()(64bit) is needed by (installed) > suitesparse-3.4.0-2.fc12.x86_64 > liblapack.so.3()(64bit) is needed by (installed) octave-6:3.2.3-4.fc12.x86_64 > liblapack.so.3()(64bit) is needed by (installed) qrupdate-1.1.1-1.fc12.x86_64 > liblapack.so.3()(64bit) is needed by (installed) > octave-forge-20090607-17.fc12.x86_64 > > How do I remove it? 'rpm -e --nodeps atlas-3.8.3-12.fc12.x86_64 atlas-3.8.3-16.fc12.x86_64'
I would suggest yum erase atlas* (that would remove lots off other things that depend on atlas) yum install atlas-sse2-3.8.3-16.fc12.x86_64.rpm (assuming you have downloaded the rpm into current directory) yum install octave (that would install octave and other deps, but should skip the old atlas) Dmitri.
PROBLEM FIXED! After yum erase atlas rpm -ivh atlas-sse2-3.8.3-16.fc12.x86_64.rpm yum install octave I have rpm -q octave atlas-sse2 atlas octave-3.2.3-4.fc12.x86_64 atlas-sse2-3.8.3-16.fc12.x86_64 package atlas is not installed And the problem is fixed on my opt AMD! Thanks! I'll also test it on our other AMD and report here.
Confirmed. This also fixes our other AMD. Case closed.
*** Bug 573074 has been marked as a duplicate of this bug. ***
Deji, I'm assuming that this doesn't require a rebuild of octave against the new atlas?
Alex, No, octave is fine.
(In reply to comment #25) > Alex, > No, octave is fine. Are you going to push updates for F-12 F-13, as well as rebuilding for rawhide (F-14)? I don't see any in bodhi, let alone commits to CVS as yet (even rawhide is still on version 3.8.3-15.fc13). Bodhi should close this bug as part of the push rather than being closed manually.
atlas-3.8.3-16.fc13 has been submitted as an update for Fedora 13. http://admin.fedoraproject.org/updates/atlas-3.8.3-16.fc13
atlas-3.8.3-14.fc12 has been submitted as an update for Fedora 12. http://admin.fedoraproject.org/updates/atlas-3.8.3-14.fc12
atlas-3.8.3-14.fc12 has been pushed to the Fedora 12 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update atlas'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/atlas-3.8.3-14.fc12
atlas-3.8.3-16.fc13 has been pushed to the Fedora 13 testing repository. If problems still persist, please make note of it in this bug report. If you want to test the update, you can install it with su -c 'yum --enablerepo=updates-testing update atlas'. You can provide feedback for this update here: http://admin.fedoraproject.org/updates/atlas-3.8.3-16.fc13
I don't have AMD, so I can't test whether this fixes the bug, but it doesn't otherwise introduce any regressions w.r.t. octave.
atlas-3.8.3-16.fc13 has been pushed to the Fedora 13 stable repository. If problems still persist, please make note of it in this bug report.
atlas-3.8.3-14.fc12 has been pushed to the Fedora 12 stable repository. If problems still persist, please make note of it in this bug report.
That fix is incorrect. The SSE2 build needs to be the default, and -sse3 in a subpackage. The default build must be the one running on all machines of the given architecture which fulfill our minimum requirements, i.e. the most generic one.
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