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Installation error for v. 3.3
Posted: Mon Oct 27, 2014 4:00 pm
by ehsan
Hi Rich,
I was checking the GYRE bitbucket page out of the blue, and came across a a fresh new version. So, thought giving it a try.
Though my installation went very well, the make test failed:
Code: Select all
TEST MESA model for beta Cephei star ...succeeded
TEST MESA model for RGB star
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x10333d742
#1 0x10333ded0
#2 0x7fff8cb985a9
#3 0x102cfc8d0
#4 0x1034c7578
#5 0x7fff8ff2d898
#6 0x7fff8ff2d729
test_support: line 19: 57754 Segmentation fault: 11 $exec $file > /dev/null
...failed during execution of ./gyre_nad
make[2]: Leaving directory `/Users/ehsan/programs/gyre3.3/test/nad'
make[1]: Leaving directory `/Users/ehsan/programs/gyre3.3/test'
(canopy) ehsan:gyre3.3 ehsan$
I use the latest sdk on Mavericks.
Any more info I may provide?
Best
Ehsan.
Re: Installation error for v. 3.3
Posted: Mon Oct 27, 2014 7:55 pm
by rhtownsend
ehsan wrote:Hi Rich,
I was checking the GYRE bitbucket page out of the blue, and came across a a fresh new version. So, thought giving it a try.
Though my installation went very well, the make test failed:
Code: Select all
TEST MESA model for beta Cephei star ...succeeded
TEST MESA model for RGB star
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x10333d742
#1 0x10333ded0
#2 0x7fff8cb985a9
#3 0x102cfc8d0
#4 0x1034c7578
#5 0x7fff8ff2d898
#6 0x7fff8ff2d729
test_support: line 19: 57754 Segmentation fault: 11 $exec $file > /dev/null
...failed during execution of ./gyre_nad
make[2]: Leaving directory `/Users/ehsan/programs/gyre3.3/test/nad'
make[1]: Leaving directory `/Users/ehsan/programs/gyre3.3/test'
(canopy) ehsan:gyre3.3 ehsan$
I use the latest sdk on Mavericks.
Any more info I may provide?
Best
Ehsan.
Serves you right for installing it before I've announced it!
Seriously, though -- are you using the new Yosemite SDK? Can you recompile with debugging enabled (edit src/Make.inc and set DEBUG=yes), and then re-run inside gdb?
That should give you an idea of where the error is.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 9:30 am
by ehsan
Sorry to act before you. I actually thought it is announced when the source file is uploaded!
Actually, the forum user does not receive update notifications, so I thought I had missed that, and directly went ahead installing the new version.
B.t.w, here are two logs of my installation and test steps.
Best
Ehsan.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 9:37 am
by rhtownsend
ehsan wrote:Sorry to act before you. I actually thought it is announced when the source file is uploaded!
Actually, the forum user does not receive update notifications, so I thought I had missed that, and directly went ahead installing the new version.
B.t.w, here are two logs of my installation and test steps.
Best
Ehsan.
Don't worry about it -- just joking with you!
Both of the files look reasonable. What you'll need to do is recompile with debugging enabled, and then run the code from within gdb. I need to see where in the code the exception is arising.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 9:49 am
by ehsan
What you'll need to do is recompile with debugging enabled, and then run the code from within gdb. I need to see where in the code the exception is arising.
Well, the log files that I sent are actually after turing on the DEBUG mode.
So, when I look at the last few lines in test.txt, it says
Code: Select all
TEST MESA model for RGB star ...failed during execution of ./gyre_nad
Is this a clear pointer for you to figure out the issue?
One more question:
What do you exactly mean by "gdb"? What shall I specifically do?
Best
Ehsan.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 9:52 am
by rhtownsend
ehsan wrote:What you'll need to do is recompile with debugging enabled, and then run the code from within gdb. I need to see where in the code the exception is arising.
Well, the log files that I sent are actually after turing on the DEBUG mode.
So, when I look at the last few lines in test.txt, it says
Code: Select all
TEST MESA model for RGB star ...failed during execution of ./gyre_nad
Is this a clear pointer for you to figure out the issue?
One more question:
What do you exactly mean by "gdb"? What shall I specifically do?
Best
Ehsan.
'gdb' is the GNU debugger. To use it in this case, take the following steps:
cd test/mesa/rgb
gdb ./gyre_nad
...and then when in gdb use:
run gyre_nad.in
You should get an indication of where and why the program crashes -- let me know what you find.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 10:26 am
by ehsan
cd test/mesa/rgb
gdb ./gyre_nad
The correct path is
But, I do not have gdb installed! Is it supposed to ship with the SDK?
Code: Select all
ehsan:rgb ehsan$ gdb ./gyre_nad
-bash: gdb: command not found
Ehsan.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 10:28 am
by rhtownsend
ehsan wrote:cd test/mesa/rgb
gdb ./gyre_nad
The correct path is
But, I do not have gdb installed! Is it supposed to ship with the SDK?
Code: Select all
ehsan:rgb ehsan$ gdb ./gyre_nad
-bash: gdb: command not found
Ehsan.
Ah -- try using lldb instead. Same procedure as above.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 10:55 am
by ehsan
I have a MacBook Pro with Mavericks, and
Code: Select all
ehsan:rgb ehsan$ gfortran --version
GNU Fortran (GCC) 4.10.0 20140710 (experimental)
Copyright (C) 2014 Free Software Foundation, Inc.
ehsan:rgb ehsan$ lldb ./gyre_nad
ImportError: No module named site
Instead, I turned into another Linux machine with the same SDK, and with gdb installed. The outcome seems pretty normal to me, though this is the first time I'm touching gdb!
Code: Select all
Root Solving
l n_pg n_p n_g Re(omega) Im(omega) chi n_iter n
3 -857 6 863 0.1144817945895822E+02 0.2286994021705236E-02 0.1149850933779768E-12 12 5472
3 -856 6 862 0.1146137919953506E+02 0.2285729165629793E-02 0.1121504910262482E-13 12 5472
3 -855 6 861 0.1147460164909394E+02 0.2280570028425316E-02 0.5193791669579645E-13 11 5472
3 -854 6 860 0.1148786279092608E+02 0.2271103896163875E-02 0.1030550773962675E-12 12 5472
3 -853 6 859 0.1150117209964801E+02 0.2260425354281123E-02 0.5429866732050625E-12 11 5472
3 -852 6 858 0.1151452771659745E+02 0.2254338712814190E-02 0.8592253034792999E-13 13 5472
3 -851 6 857 0.1152791088341125E+02 0.2254982464887498E-02 0.3067733810454298E-12 13 5472
3 -850 6 856 0.1154131225706396E+02 0.2255783784324068E-02 0.6895164621079761E-13 14 5472
3 -849 6 855 0.1155473706172467E+02 0.2249971320976144E-02 0.2550092780337752E-12 12 5472
3 -848 6 854 0.1156820371140219E+02 0.2236148594189632E-02 0.1892407620106035E-12 11 5472
3 -847 6 853 0.1158171652815153E+02 0.2224424541355242E-02 0.8932454058560952E-13 8 5472
3 -846 6 852 0.1159525699931610E+02 0.2223199078689341E-02 0.1180985345257655E-12 11 5472
3 -845 6 851 0.1160880058508546E+02 0.2229054795115745E-02 0.1510269361073275E-12 10 5472
3 -844 6 850 0.1162234997932599E+02 0.2228621027379685E-02 0.3019834581594359E-12 11 5472
3 -843 6 849 0.1163593509555049E+02 0.2215875139423742E-02 0.1866870854199175E-13 10 5472
3 -842 6 848 0.1164958533721142E+02 0.2199441067908136E-02 0.1064983544825574E-12 13 5472
3 -841 6 847 0.1166329311329756E+02 0.2193435756639105E-02 0.2729501866835559E-13 13 5472
3 -840 6 846 0.1167702813457729E+02 0.2198906589846548E-02 0.1066553046719234E-12 10 5472
3 -839 6 845 0.1169077586984510E+02 0.2202702674281849E-02 0.2777162492122962E-13 10 5472
3 -838 6 844 0.1170455266109434E+02 0.2193420784351936E-02 0.7393407105867424E-13 14 5472
3 -837 6 843 0.1171838339331549E+02 0.2175247844291213E-02 0.7755475932027344E-13 12 5472
3 -836 6 842 0.1173226605698112E+02 0.2163805019166780E-02 0.3915043835148591E-13 10 5472
3 -835 6 841 0.1174616433859328E+02 0.2166795436893818E-02 0.1737992118604040E-12 9 5472
3 -834 6 840 0.1176005075733232E+02 0.2175415888488144E-02 0.1267668466788115E-12 11 5472
3 -833 6 839 0.1177393567022204E+02 0.2174274389787915E-02 0.8923031649752275E-13 14 5472
3 -832 6 838 0.1178786459308901E+02 0.2157808196063391E-02 0.1500527171392261E-12 9 5472
3 -831 6 837 0.1180187035483705E+02 0.2140306890708961E-02 0.1008489677456336E-12 11 5472
3 -830 6 836 0.1181594093403558E+02 0.2134769634809985E-02 0.1951703193101227E-12 9 5472
3 -829 6 835 0.1183003914565979E+02 0.2141132079570330E-02 0.2865570329565852E-12 12 5472
3 -828 6 834 0.1184414821159293E+02 0.2145454763910063E-02 0.5373642026046090E-13 13 5472
3 -827 6 833 0.1185828140034025E+02 0.2137099891040799E-02 0.4062660423519781E-12 12 5472
3 -826 6 832 0.1187246766836151E+02 0.2120403515822316E-02 0.1452465905790826E-12 9 5472
3 -825 6 831 0.1188670555611791E+02 0.2109473357855642E-02 0.4449722918284672E-13 8 5472
3 -824 6 830 0.1190096704799703E+02 0.2111812062078141E-02 0.5668053613244353E-13 16 5472
3 -823 6 829 0.1191522836455900E+02 0.2118625409491305E-02 0.1304864778588246E-12 13 5472
3 -822 6 828 0.1192949894261694E+02 0.2116284283864636E-02 0.6343340074640617E-13 10 5472
3 -821 6 827 0.1194382052486406E+02 0.2100604923452432E-02 0.5796637618296436E-13 10 5472
3 -820 6 826 0.1195821331332472E+02 0.2083866122463935E-02 0.1231391518571670E-12 9 5472
3 -819 6 825 0.1197266381387873E+02 0.2078245588733754E-02 0.2958031757101249E-13 13 5472
3 -818 6 824 0.1198713016920363E+02 0.2085186104524060E-02 0.2344078022076096E-12 10 5472
3 -817 6 823 0.1200159570508176E+02 0.2091069053477738E-02 0.4054548407672936E-12 10 5472
3 -816 7 823 0.1201607908528812E+02 0.2084073685591969E-02 0.2181881539082880E-12 8 5472
3 -815 7 822 0.1203062384475594E+02 0.2066447301336070E-02 0.3431048486469601E-12 9 5472
Time elapsed : 513.526 s
[Inferior 1 (process 31388) exited normally]
Missing separate debuginfos, use: debuginfo-install glibc-2.17-21.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64
(gdb)
Does it tell you enough to start debugging?
Shall I do extra?
Do I have to ask our system admins to install: debuginfo-install glibc-2.17-21.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64 ?
Ehsan.
Re: Installation error for v. 3.3
Posted: Tue Oct 28, 2014 10:58 am
by rhtownsend
ehsan wrote:I have a MacBook Pro with Mavericks, and
Code: Select all
ehsan:rgb ehsan$ gfortran --version
GNU Fortran (GCC) 4.10.0 20140710 (experimental)
Copyright (C) 2014 Free Software Foundation, Inc.
ehsan:rgb ehsan$ lldb ./gyre_nad
ImportError: No module named site
Instead, I turned into another Linux machine with the same SDK, and with gdb installed. The outcome seems pretty normal to me, though this is the first time I'm touching gdb!
Code: Select all
Root Solving
l n_pg n_p n_g Re(omega) Im(omega) chi n_iter n
3 -857 6 863 0.1144817945895822E+02 0.2286994021705236E-02 0.1149850933779768E-12 12 5472
3 -856 6 862 0.1146137919953506E+02 0.2285729165629793E-02 0.1121504910262482E-13 12 5472
3 -855 6 861 0.1147460164909394E+02 0.2280570028425316E-02 0.5193791669579645E-13 11 5472
3 -854 6 860 0.1148786279092608E+02 0.2271103896163875E-02 0.1030550773962675E-12 12 5472
3 -853 6 859 0.1150117209964801E+02 0.2260425354281123E-02 0.5429866732050625E-12 11 5472
3 -852 6 858 0.1151452771659745E+02 0.2254338712814190E-02 0.8592253034792999E-13 13 5472
3 -851 6 857 0.1152791088341125E+02 0.2254982464887498E-02 0.3067733810454298E-12 13 5472
3 -850 6 856 0.1154131225706396E+02 0.2255783784324068E-02 0.6895164621079761E-13 14 5472
3 -849 6 855 0.1155473706172467E+02 0.2249971320976144E-02 0.2550092780337752E-12 12 5472
3 -848 6 854 0.1156820371140219E+02 0.2236148594189632E-02 0.1892407620106035E-12 11 5472
3 -847 6 853 0.1158171652815153E+02 0.2224424541355242E-02 0.8932454058560952E-13 8 5472
3 -846 6 852 0.1159525699931610E+02 0.2223199078689341E-02 0.1180985345257655E-12 11 5472
3 -845 6 851 0.1160880058508546E+02 0.2229054795115745E-02 0.1510269361073275E-12 10 5472
3 -844 6 850 0.1162234997932599E+02 0.2228621027379685E-02 0.3019834581594359E-12 11 5472
3 -843 6 849 0.1163593509555049E+02 0.2215875139423742E-02 0.1866870854199175E-13 10 5472
3 -842 6 848 0.1164958533721142E+02 0.2199441067908136E-02 0.1064983544825574E-12 13 5472
3 -841 6 847 0.1166329311329756E+02 0.2193435756639105E-02 0.2729501866835559E-13 13 5472
3 -840 6 846 0.1167702813457729E+02 0.2198906589846548E-02 0.1066553046719234E-12 10 5472
3 -839 6 845 0.1169077586984510E+02 0.2202702674281849E-02 0.2777162492122962E-13 10 5472
3 -838 6 844 0.1170455266109434E+02 0.2193420784351936E-02 0.7393407105867424E-13 14 5472
3 -837 6 843 0.1171838339331549E+02 0.2175247844291213E-02 0.7755475932027344E-13 12 5472
3 -836 6 842 0.1173226605698112E+02 0.2163805019166780E-02 0.3915043835148591E-13 10 5472
3 -835 6 841 0.1174616433859328E+02 0.2166795436893818E-02 0.1737992118604040E-12 9 5472
3 -834 6 840 0.1176005075733232E+02 0.2175415888488144E-02 0.1267668466788115E-12 11 5472
3 -833 6 839 0.1177393567022204E+02 0.2174274389787915E-02 0.8923031649752275E-13 14 5472
3 -832 6 838 0.1178786459308901E+02 0.2157808196063391E-02 0.1500527171392261E-12 9 5472
3 -831 6 837 0.1180187035483705E+02 0.2140306890708961E-02 0.1008489677456336E-12 11 5472
3 -830 6 836 0.1181594093403558E+02 0.2134769634809985E-02 0.1951703193101227E-12 9 5472
3 -829 6 835 0.1183003914565979E+02 0.2141132079570330E-02 0.2865570329565852E-12 12 5472
3 -828 6 834 0.1184414821159293E+02 0.2145454763910063E-02 0.5373642026046090E-13 13 5472
3 -827 6 833 0.1185828140034025E+02 0.2137099891040799E-02 0.4062660423519781E-12 12 5472
3 -826 6 832 0.1187246766836151E+02 0.2120403515822316E-02 0.1452465905790826E-12 9 5472
3 -825 6 831 0.1188670555611791E+02 0.2109473357855642E-02 0.4449722918284672E-13 8 5472
3 -824 6 830 0.1190096704799703E+02 0.2111812062078141E-02 0.5668053613244353E-13 16 5472
3 -823 6 829 0.1191522836455900E+02 0.2118625409491305E-02 0.1304864778588246E-12 13 5472
3 -822 6 828 0.1192949894261694E+02 0.2116284283864636E-02 0.6343340074640617E-13 10 5472
3 -821 6 827 0.1194382052486406E+02 0.2100604923452432E-02 0.5796637618296436E-13 10 5472
3 -820 6 826 0.1195821331332472E+02 0.2083866122463935E-02 0.1231391518571670E-12 9 5472
3 -819 6 825 0.1197266381387873E+02 0.2078245588733754E-02 0.2958031757101249E-13 13 5472
3 -818 6 824 0.1198713016920363E+02 0.2085186104524060E-02 0.2344078022076096E-12 10 5472
3 -817 6 823 0.1200159570508176E+02 0.2091069053477738E-02 0.4054548407672936E-12 10 5472
3 -816 7 823 0.1201607908528812E+02 0.2084073685591969E-02 0.2181881539082880E-12 8 5472
3 -815 7 822 0.1203062384475594E+02 0.2066447301336070E-02 0.3431048486469601E-12 9 5472
Time elapsed : 513.526 s
[Inferior 1 (process 31388) exited normally]
Missing separate debuginfos, use: debuginfo-install glibc-2.17-21.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64
(gdb)
Does it tell you enough to start debugging?
Shall I do extra?
Do I have to ask our system admins to install: debuginfo-install glibc-2.17-21.fc19.x86_64 zlib-1.2.7-10.fc19.x86_64 ?
Ehsan.
What this tells me is that the code runs fine on the Linux machine!
Unless I'm able to reproduce the bug, or unless you're able to figure out where in the code the bug is happening, I'm afraid I can't be of much assistance.