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finottiOffline
Post subject: [Solved] MAGMA not working with kernel 4.4  PostPosted: 02.02.2016, 20:15



Joined: 2010-09-12
Posts: 470

Status: Offline
I use a closed source math software called MAGMA (http://magma.maths.usyd.edu.au/magma/) for work. I never had a problem with it, but now I get:

      Code:

finottim83[/usr/local/magma-02.21-6]$ magma
Segmentation fault


I've tried many versions of MAGMA, and all give segmentation fault. I tried older kernels and 4.3 and back work. I also tried linux-image-4.4.0-trunk-amd64 (from experimental) and it also works. But none of the slh 4.4 kernels I have work:

      Code:

root@finottim83[/usr/local/magma-02.21-10]# dpkg-query -l | grep linux-image-4.4
ii  linux-image-4.4.0-0.slh.1-aptosid-amd64       4.4-2                                  amd64        Linux 4.4 for 64-bit PCs
ii  linux-image-4.4.0-0.slh.2-aptosid-amd64       4.4-3                                  amd64        Linux 4.4 for 64-bit PCs
ii  linux-image-4.4.0-0.slh.3-aptosid-amd64       4.4-4                                  amd64        Linux 4.4 for 64-bit PCs
ii  linux-image-4.4.0-1.slh.1-aptosid-amd64       4.4-5                                  amd64        Linux 4.4 for 64-bit PCs
ii  linux-image-4.4.0-trunk-amd64                 4.4-1~exp1                             amd64        Linux 4.4 for 64-bit PCs


The same is true for my laptop and home desktop (although I haven't tried the trunk kernel with them).

I am not sure how to provide useful information to debug it, but I'd be glad to do whatever I can. This software is important to me, so any help would be appreciated.

Best,

Luis

Edit: I'm not sure this helps, but here is the output of "strace -v magma"

      Code:

execve("/usr/local/bin/magma", ["magma"], ["XDG_VTNR=7", "SSH_AGENT_PID=2482", "XDG_SESSION_ID=2", "KDE_MULTIHEAD=false", "HOST=t510", "TERM=xterm", "SHELL=/bin/bash", "XDG_SESSION_COOKIE=0b1bd89264bdc"..., "GTK2_RC_FILES=/etc/gtk-2.0/gtkrc"..., "KONSOLE_DBUS_SERVICE=:1.41", "QT_LINUX_ACCESSIBILITY_ALWAYS_ON"..., "KONSOLE_PROFILE_NAME=Shell", "GTK_RC_FILES=/etc/gtk/gtkrc:/hom"..., "GS_LIB=/home/finotti/.fonts", "WINDOWID=71303173", "SHELL_SESSION_ID=a460fcd84308400"..., "lap=finotti@localhost", "LC_ALL=en_US.UTF-8", "KDE_FULL_SESSION=true", "XDG_SESSION_CLASS=user", "USER=finotti", "LS_COLORS=rs=0:di=01;34:ln=01;36"..., "QT_ACCESSIBILITY=1", "XDG_SESSION_PATH=/org/freedeskto"..., "SAGE_BROWSER=/usr/bin/iceweasel "..., "XDG_SEAT_PATH=/org/freedesktop/D"..., "SSH_AUTH_SOCK=/tmp/ssh-tG0bOpg87"..., "SESSION_MANAGER=local/t510:@/tmp"..., "PAGER=less", "XEDITOR=/home/finotti/bin/em", "DESKTOP_SESSION=/usr/share/xsess"..., "PATH=/usr/bin:/bin:/usr/local/bi"..., "QT_IM_MODULE=compose", "XDG_SESSION_TYPE=x11", "PWD=/home/finotti", "desk=finotti@finotti.no-ip.biz", "EDITOR=/home/finotti/bin/em", "KDE_SESSION_UID=1000", "LANG=en_US.UTF-8", "PS1=\\h[\\w]\\$ ", "PAPERSIZE=letter", "KONSOLE_DBUS_SESSION=/Sessions/2", "utk=finotti@agnesi.math.utk.edu", "HISTCONTROL=erasedups", "PS2=> ", "HOME=/home/finotti", "SHLVL=1", "COLORFGBG=15;0", "XDG_SEAT=seat0", "LANGUAGE=", "KDE_SESSION_VERSION=5", "XCURSOR_THEME=breeze_cursors", "deskh=finotti@192.168.1.120", "LESS=r", "LOGNAME=finotti", "XDG_SESSION_DESKTOP=KDE", "PRINTER=UT2", "VISUAL=nano -wk", "XDG_DATA_DIRS=/usr/share:/usr/sh"..., "DBUS_SESSION_BUS_ADDRESS=unix:ab"..., "BROWSER=/usr/bin/iceweasel -P de"..., "PROFILEHOME=", "XDG_RUNTIME_DIR=/run/user/1000", "DISPLAY=:0", "GTK_IM_MODULE=xim", "XDG_CURRENT_DESKTOP=KDE", "TROFF=groff", "HISTTIMEFORMAT=%h/%d - %H:%M:%S ", "XAUTHORITY=/tmp/xauth-1000-_0", "_=/usr/bin/strace"]) = 0
brk(NULL)                               = 0x55580cc2b000
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
mmap(NULL, 8192, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f313de70000
access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 3
fstat(3, {st_dev=makedev(8, 2), st_ino=2556, st_mode=S_IFREG|0644, st_nlink=1, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=552, st_size=282263, st_atime=2016/02/02-14:54:50.911417234, st_mtime=2016/02/02-14:54:50.912417266, st_ctime=2016/02/02-14:54:50.916417393}) = 0
mmap(NULL, 282263, PROT_READ, MAP_PRIVATE, 3, 0) = 0x7f313de2b000
close(3)                                = 0
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)
open("/lib/x86_64-linux-gnu/libc.so.6", O_RDONLY|O_CLOEXEC) = 3
read(3, "\177ELF\2\1\1\3\0\0\0\0\0\0\0\0\3\0>\0\1\0\0\0\220\t\2\0\0\0\0\0"..., 832) = 832
fstat(3, {st_dev=makedev(8, 2), st_ino=135668, st_mode=S_IFREG|0755, st_nlink=1, st_uid=0, st_gid=0, st_blksize=4096, st_blocks=3344, st_size=1710168, st_atime=2016/01/26-08:59:03, st_mtime=2016/01/23-19:31:51, st_ctime=2016/01/26-08:59:27.956455367}) = 0
mmap(NULL, 3817216, PROT_READ|PROT_EXEC, MAP_PRIVATE|MAP_DENYWRITE, 3, 0) = 0x7f313d8ad000
mprotect(0x7f313da47000, 2097152, PROT_NONE) = 0
mmap(0x7f313dc47000, 24576, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_DENYWRITE, 3, 0x19a000) = 0x7f313dc47000
mmap(0x7f313dc4d000, 16128, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_FIXED|MAP_ANONYMOUS, -1, 0) = 0x7f313dc4d000
close(3)                                = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f313de2a000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f313de29000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7f313de28000
arch_prctl(ARCH_SET_FS, 0x7f313de29700) = 0
mprotect(0x7f313dc47000, 16384, PROT_READ) = 0
mprotect(0x55580b6a1000, 8192, PROT_READ) = 0
mprotect(0x7f313de72000, 4096, PROT_READ) = 0
munmap(0x7f313de2b000, 282263)          = 0
getpid()                                = 11068
rt_sigaction(SIGCHLD, {0x55580b498c20, ~[RTMIN RT_1], SA_RESTORER, 0x7f313d8e0590}, NULL, 8) = 0
geteuid()                               = 1000
brk(NULL)                               = 0x55580cc2b000
brk(0x55580cc4c000)                     = 0x55580cc4c000
getppid()                               = 11066
stat("/home/finotti", {st_dev=makedev(8, 4), st_ino=2228225, st_mode=S_IFDIR|0755, st_nlink=174, st_uid=1000, st_gid=1000, st_blksize=4096, st_blocks=40, st_size=20480, st_atime=2011/12/05-17:52:15.253459121, st_mtime=2016/02/02-16:00:17.856055009, st_ctime=2016/02/02-16:00:17.856055009}) = 0
stat(".", {st_dev=makedev(8, 4), st_ino=2228225, st_mode=S_IFDIR|0755, st_nlink=174, st_uid=1000, st_gid=1000, st_blksize=4096, st_blocks=40, st_size=20480, st_atime=2011/12/05-17:52:15.253459121, st_mtime=2016/02/02-16:00:17.856055009, st_ctime=2016/02/02-16:00:17.856055009}) = 0
open("/usr/local/bin/magma", O_RDONLY)  = 3
fcntl(3, F_DUPFD, 10)                   = 11
close(3)                                = 0
fcntl(11, F_SETFD, FD_CLOEXEC)          = 0
rt_sigaction(SIGINT, NULL, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGINT, {0x55580b498c20, ~[RTMIN RT_1], SA_RESTORER, 0x7f313d8e0590}, NULL, 8) = 0
rt_sigaction(SIGQUIT, NULL, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGQUIT, {SIG_DFL, ~[RTMIN RT_1], SA_RESTORER, 0x7f313d8e0590}, NULL, 8) = 0
rt_sigaction(SIGTERM, NULL, {SIG_DFL, [], 0}, 8) = 0
rt_sigaction(SIGTERM, {SIG_DFL, ~[RTMIN RT_1], SA_RESTORER, 0x7f313d8e0590}, NULL, 8) = 0
read(11, "#!/bin/sh\n\nROOT=\"/usr/local/magm"..., 8192) = 1243
stat("/home/finotti/.magmarc", 0x7ffc3dc63db0) = -1 ENOENT (No such file or directory)
pipe([3, 4])                            = 0
clone(child_stack=0, flags=CLONE_CHILD_CLEARTID|CLONE_CHILD_SETTID|SIGCHLD, child_tidptr=0x7f313de299d0) = 11069
close(4)                                = 0
read(3, "Linux\n", 128)                 = 6
read(3, "", 128)                        = 0
close(3)                                = 0
--- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_EXITED, si_pid=11069, si_uid=1000, si_status=0, si_utime=0, si_stime=0} ---
rt_sigreturn({mask=[]})                 = 0
wait4(-1, [{WIFEXITED(s) && WEXITSTATUS(s) == 0}], 0, NULL) = 11069
execve("/usr/local/magma-2.20-4/magma.exe", ["/usr/local/magma-2.20-4/magma.ex"...], ["KDE_FULL_SESSION=true", "PROFILEHOME=", "GS_LIB=/home/finotti/.fonts", "XEDITOR=/home/finotti/bin/em", "HISTTIMEFORMAT=%h/%d - %H:%M:%S ", "USER=finotti", "LANGUAGE=", "MAGMAPASSFILE=/usr/local/magma-2"..., "XDG_SEAT=seat0", "SSH_AGENT_PID=2482", "XDG_SESSION_TYPE=x11", "SHLVL=1", "BROWSER=/usr/bin/iceweasel -P de"..., "HOME=/home/finotti", "LESS=r", "XDG_SESSION_COOKIE=0b1bd89264bdc"..., "DESKTOP_SESSION=/usr/share/xsess"..., "MAGMA_HTML_DIR=/usr/local/magma-"..., "QT_LINUX_ACCESSIBILITY_ALWAYS_ON"..., "GTK_RC_FILES=/etc/gtk/gtkrc:/hom"..., "SHELL_SESSION_ID=a460fcd84308400"..., "XDG_SEAT_PATH=/org/freedesktop/D"..., "PAGER=less", "KDE_SESSION_VERSION=5", "PS1=\\h[\\w]\\$ ", "KONSOLE_DBUS_SESSION=/Sessions/2", "PS2=> ", "VISUAL=nano -wk", "DBUS_SESSION_BUS_ADDRESS=unix:ab"..., "MAGMA_LIBRARIES=examples:galpols"..., "TROFF=groff", "LOGNAME=finotti", "GTK_IM_MODULE=xim", "WINDOWID=71303173", "_=/usr/bin/strace", "KONSOLE_PROFILE_NAME=Shell", "lap=finotti@localhost", "XDG_SESSION_CLASS=user", "COLORFGBG=15;0", "XDG_SESSION_ID=2", "TERM=xterm", "GTK2_RC_FILES=/etc/gtk-2.0/gtkrc"..., "HISTCONTROL=erasedups", "PATH=/usr/bin:/bin:/usr/local/bi"..., "SESSION_MANAGER=local/t510:@/tmp"..., "PAPERSIZE=letter", "deskh=finotti@192.168.1.120", "MAGMA_LIBRARY_ROOT=/usr/local/ma"..., "XDG_SESSION_PATH=/org/freedeskto"..., "XCURSOR_THEME=breeze_cursors", "XDG_RUNTIME_DIR=/run/user/1000", "DISPLAY=:0", "LANG=en_US.UTF-8", "XDG_CURRENT_DESKTOP=KDE", "LS_COLORS=rs=0:di=01;34:ln=01;36"..., "XDG_SESSION_DESKTOP=KDE", "XAUTHORITY=/tmp/xauth-1000-_0", "SSH_AUTH_SOCK=/tmp/ssh-tG0bOpg87"..., "MAGMA_SYSTEM_SPEC=/usr/local/mag"..., "HOST=t510", "SHELL=/bin/bash", "QT_ACCESSIBILITY=1", "utk=finotti@agnesi.math.utk.edu", "KONSOLE_DBUS_SERVICE=:1.41", "KDE_MULTIHEAD=false", "XDG_VTNR=7", "QT_IM_MODULE=compose", "LC_ALL=en_US.UTF-8", "PWD=/home/finotti", "desk=finotti@finotti.no-ip.biz", "PRINTER=UT2", "XDG_DATA_DIRS=/usr/share:/usr/sh"..., "MAGMA_HELP_DIR=/usr/local/magma-"..., "SAGE_BROWSER=/usr/bin/iceweasel "..., "KDE_SESSION_UID=1000", "EDITOR=/home/finotti/bin/em"]) = 0
uname({sysname="Linux", nodename="t510", release="4.4.0-1.slh.1-aptosid-amd64", version="#1 SMP PREEMPT aptosid 4.4-5 (2016-02-02)", machine="x86_64", domainname="(none)"}) = 0
brk(NULL)                               = 0x402d000
brk(0x402e1a0)                          = 0x402e1a0
arch_prctl(ARCH_SET_FS, 0x402d880)      = 0
set_tid_address(0x402db50)              = 11068
set_robust_list(0x402db60, 24)          = 0
futex(0x7fffc7a57f3c, FUTEX_WAKE_PRIVATE, 1) = 0
futex(0x7fffc7a57f3c, FUTEX_WAIT_BITSET_PRIVATE|FUTEX_CLOCK_REALTIME, 1, NULL, 402d880) = -1 EAGAIN (Resource temporarily unavailable)
rt_sigaction(SIGRTMIN, {0x1bf6230, [], SA_RESTORER|SA_SIGINFO, 0x1bff750}, NULL, 8) = 0
rt_sigaction(SIGRT_1, {0x1bf6160, [], SA_RESTORER|SA_RESTART|SA_SIGINFO, 0x1bff750}, NULL, 8) = 0
rt_sigprocmask(SIG_UNBLOCK, [RTMIN RT_1], NULL, 8) = 0
getrlimit(RLIMIT_STACK, {rlim_cur=8192*1024, rlim_max=RLIM64_INFINITY}) = 0
brk(0x404f1a0)                          = 0x404f1a0
brk(0x4050000)                          = 0x4050000
mmap(NULL, 33587200, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, 0, 0) = 0x7fb74b0c1000
mmap(NULL, 65536, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, 0, 0) = 0x7fb74b0b1000
socket(PF_INET, SOCK_DGRAM, IPPROTO_IP) = 3
open("/proc/net/dev", O_RDONLY)         = 4
fstat(4, {st_dev=makedev(0, 4), st_ino=4026531972, st_mode=S_IFREG|0444, st_nlink=1, st_uid=0, st_gid=0, st_blksize=1024, st_blocks=0, st_size=0, st_atime=2016/02/02-16:00:31.249489079, st_mtime=2016/02/02-16:00:31.249489079, st_ctime=2016/02/02-16:00:31.249489079}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) = 0x7fb74b0b0000
read(4, "Inter-|   Receive               "..., 1024) = 692
ioctl(3, SIOCGIFHWADDR, {ifr_name="eth0", ifr_hwaddr=5c:ff:35:01:59:f1}) = 0
ioctl(3, SIOCGIFHWADDR, {ifr_name="wlan0", ifr_hwaddr=00:23:14:98:0d:88}) = 0
ioctl(3, SIOCGIFHWADDR, {ifr_name="lo", ifr_hwaddr=00:00:00:00:00:00}) = 0
ioctl(3, SIOCGIFHWADDR, {ifr_name="tun0", ifr_hwaddr=00:00:00:00:00:00}) = 0
read(4, "", 1024)                       = 0
--- SIGSEGV {si_signo=SIGSEGV, si_code=SEGV_MAPERR, si_addr=0xffffffffff600400} ---
+++ killed by SIGSEGV +++



Last edited by finotti on 25.02.2016, 13:56; edited 1 time in total
 
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elishOffline
Post subject: RE: MAGMA not working with kernel 4.4  PostPosted: 03.02.2016, 18:32



Joined: 2013-11-09
Posts: 33

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Never heard of it, how is it different from GNU Octave?
https://www.gnu.org/software/octave/
 
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finottiOffline
Post subject: RE: MAGMA not working with kernel 4.4  PostPosted: 03.02.2016, 19:58



Joined: 2010-09-12
Posts: 470

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Hi elish,

It's very different. Octave, as a Matlab clone, is built around matrices ("MATrix LAB") and it's useful for many applications. MAGMA is stronger in number theory and arithmetic geometry, and it's the most advanced software for those areas. Sage (http://www.sagemath.org/) is an open source alternative and it is great. I use it quite a bit, but I have a lot of code written for MAGMA that I need...

It's a shame that MAGMA is closed source... In fact, that's why Sage was first created.

Luis
 
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elishOffline
Post subject: RE: MAGMA not working with kernel 4.4  PostPosted: 03.02.2016, 20:10



Joined: 2013-11-09
Posts: 33

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Good to know, thanks.
I had a chance to play a little with Matlab and Maple.
Hope the problem will be solved quickly.
 
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finottiOffline
Post subject: RE: MAGMA not working with kernel 4.4  PostPosted: 25.02.2016, 13:56



Joined: 2010-09-12
Posts: 470

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With the help of a MAGMA developer, we found out that dynamically linked version works with slh's 4.4 kernels. In the previous versions, the statically linked version always worked...

Any reason why the new 4.4 kernels would have an effect on that? (Again, Debian's trunk 4.4 kernel also works with the statically linked versions of MAGMA.)

In any case, I will mark this as solved.
 
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