Re: [gmx-users] can not pass gmxtest
Li Qiang wrote: hi, I just try to remove and rebuild and install GROMACS. This time the self-built one also can not pass the test. The same errors are reported: + [EMAIL PROTECTED]:~/gromacs-3.3.2$ sudo make tests As a general rule, do not do installations and tests of installations as root. This makes it very easy to break your system. One symptom of a broken system is things not working any more. Sound familiar? If you have a need to install as root, then do the unpack, configure & make (& make test) in your user space as yourself, and then sudo make install. This is just sensible... if someone messes up (the distributor, or more likely you) you'd much rather not be root. (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \ else echo "No gmxtest directory found. Please download and unpack it here.";\ fi) *** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8 Perhaps the authors can suggest whether gmxtest.pl uses the GROMACS binary from the same source tree, or whichever is pointed to by GMXLIB. If the latter, then you probably still have something broken somewhere. On the above sudo evidence, I'd actually be tempted to scorched-earth your machine and re-install your OS rather than mess around any more. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not pass gmxtest
hi, I just try to remove and rebuild and install GROMACS. This time the self-built one also can not pass the test. The same errors are reported: + [EMAIL PROTECTED]:~/gromacs-3.3.2$ sudo make tests (if test -d "gmxtest"; then cd "gmxtest"; ./gmxtest.pl all; cd ..; \ else echo "No gmxtest directory found. Please download and unpack it here.";\ fi) *** glibc detected *** mdrun: realloc(): invalid next size: 0x08296ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0x401b1b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0x401b3a66] mdrun[0x8137065] === Memory map: 08048000-08278000 r-xp 08:04 2567562/usr/local/gromacs/bin/mdrun 08278000-0827f000 rwxp 0023 08:04 2567562/usr/local/gromacs/bin/mdrun 0827f000-082a5000 rwxp 0827f000 00:00 0 [heap] 4000-4001a000 r-xp 08:04 2747274/lib/ld-2.6.1.so 4001a000-4001c000 rwxp 00019000 08:04 2747274/lib/ld-2.6.1.so 4001c000-4001f000 rwxp 4001c000 00:00 0 4001f000-40029000 r-xp 08:04 2747267/lib/libgcc_s.so.1 40029000-4002a000 rwxp a000 08:04 2747267/lib/libgcc_s.so.1 4002c000-4004 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so 4004-40042000 rwxp 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so 40042000-40044000 rwxp 40042000 00:00 0 40044000-4011b000 r-xp 08:04 2488482/usr/lib/libfftw3f.so.3.1.2 4011b000-40121000 rwxp 000d7000 08:04 2488482/usr/lib/libfftw3f.so.3.1.2 40121000-40144000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so 40144000-40146000 rwxp 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so 40146000-4028a000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028a000-4028b000 r-xp 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028b000-4028d000 rwxp 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so 4028d000-40291000 rwxp 4028d000 00:00 0 40291000-402a5000 r-xp 08:04 2747231/lib/tls/i686/cmov/libpthread-2.6.1.so 402a5000-402a7000 rwxp 00013000 08:04 2747231/lib/tls/i686/cmov/libpthread-2.6.1.so 402a7000-402aa000 rwxp 402a7000 00:00 0 4030-40321000 rwxp 4030 00:00 0 40321000-4040 ---p 40321000 00:00 0 bf808000-bf82 rwxp bf808000 00:00 0 [stack] e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED + On Wed, 2007-11-07 at 16:45 +0800, Yang Ye wrote: > To "uninstall" GROMACS, you can type "which mdrun" to get its path and > try to figure out where it has been installed. For GROMACS, it may > reside under > /usr/local/gromacs > > remove the whole directory with rm -fr. > > To ensure that you are using the self-built GROMACS, look for a file > > GMXRC.bash in the locations which you can find in "make install". > > Run it with > source /path/to/GMXRC.bash > > Then you can make sure that you are using your own version. > > Put that line "source ..." into ~/.bashrc shall make it default for > every login session. > > Regards, > Yang Ye > > On 11/7/2007 4:35 PM, Li Qiang wrote: > > hi yang, > > > > thanks for the reply. Do you mean that the installation from SMP is not > > right? > > > > The error with self-compiled gromacs is in position restrain step with > > unusual distances and the mdrun stops at step0 with "Segmentation fault > > (core dumped)". but the mdrun with constraint can run, though I do not > > know if it is right. > > > > The possible reason is that I install from SMP of ubuntu but forget to > > remove the self-compiled one. Several days ago the gromacs version from > > SMP is 3.3.1. I though it was simpler to install GROMACS automatically > > from that. > > > > Could tell me how to remove GROMACS entirely so that I can reinstall > > from fresh? Hope we can do it. > > > > thank you very much. > > > > Li Qiang > > > > On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: > > > >> Hi, > >> > >> You shall always try to build gromacs yourself. What's the error with > >> tutorial? > >> > >> Regards, > >> Yang Ye > >> > >> On 11/7/2007 10:14 AM, Li Qiang wrote: > >> > >>> hi all, > >>> > >>> I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package > >>> Manager(SPM). However, it can not pass the gamxtest with log as below, > >>> but Tutorials seems OK. > >>> Actually I try to compile myself at the beginning. It is weird that the > >>> self-compiled one can pass the test but failed to run Tutorials with > >>> Segmental fault at PR MD step. > >>> > >>> Does anyboby know how to solve it? and how to uninstall GROMACS clear? > >>> thanks a lot. > >>> > >>> output from gmxtest: > >>> ++ > >>> ***
Re: [gmx-users] can not pass gmxtest
To "uninstall" GROMACS, you can type "which mdrun" to get its path and try to figure out where it has been installed. For GROMACS, it may reside under /usr/local/gromacs remove the whole directory with rm -fr. To ensure that you are using the self-built GROMACS, look for a file GMXRC.bash in the locations which you can find in "make install". Run it with source /path/to/GMXRC.bash Then you can make sure that you are using your own version. Put that line "source ..." into ~/.bashrc shall make it default for every login session. Regards, Yang Ye On 11/7/2007 4:35 PM, Li Qiang wrote: hi yang, thanks for the reply. Do you mean that the installation from SMP is not right? The error with self-compiled gromacs is in position restrain step with unusual distances and the mdrun stops at step0 with "Segmentation fault (core dumped)". but the mdrun with constraint can run, though I do not know if it is right. The possible reason is that I install from SMP of ubuntu but forget to remove the self-compiled one. Several days ago the gromacs version from SMP is 3.3.1. I though it was simpler to install GROMACS automatically from that. Could tell me how to remove GROMACS entirely so that I can reinstall from fresh? Hope we can do it. thank you very much. Li Qiang On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: Hi, You shall always try to build gromacs yourself. What's the error with tutorial? Regards, Yang Ye On 11/7/2007 10:14 AM, Li Qiang wrote: hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp
Re: [gmx-users] can not pass gmxtest
hi yang, thanks for the reply. Do you mean that the installation from SMP is not right? The error with self-compiled gromacs is in position restrain step with unusual distances and the mdrun stops at step0 with "Segmentation fault (core dumped)". but the mdrun with constraint can run, though I do not know if it is right. The possible reason is that I install from SMP of ubuntu but forget to remove the self-compiled one. Several days ago the gromacs version from SMP is 3.3.1. I though it was simpler to install GROMACS automatically from that. Could tell me how to remove GROMACS entirely so that I can reinstall from fresh? Hope we can do it. thank you very much. Li Qiang On Wed, 2007-11-07 at 16:16 +0800, Yang Ye wrote: > Hi, > > You shall always try to build gromacs yourself. What's the error with > tutorial? > > Regards, > Yang Ye > > On 11/7/2007 10:14 AM, Li Qiang wrote: > > hi all, > > > > I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package > > Manager(SPM). However, it can not pass the gamxtest with log as below, > > but Tutorials seems OK. > > Actually I try to compile myself at the beginning. It is weird that the > > self-compiled one can pass the test but failed to run Tutorials with > > Segmental fault at PR MD step. > > > > Does anyboby know how to solve it? and how to uninstall GROMACS clear? > > thanks a lot. > > > > output from gmxtest: > > ++ > > *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 > > *** > > === Backtrace: = > > /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] > > /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] > > /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] > > /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] > > mdrun[0x8059f50] > > mdrun[0x805a72a] > > /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] > > mdrun[0x804a491] > > === Memory map: > > 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun > > 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun > > 08063000-08085000 rw-p 08063000 00:00 0 [heap] > > b780-b7821000 rw-p b780 00:00 0 > > b7821000-b790 ---p b7821000 00:00 0 > > b79cc000-b79cd000 rw-p b79cc000 00:00 0 > > b79cd000-b79cf000 r-xp 08:04 > > 2747181/lib/tls/i686/cmov/libdl-2.6.1.so > > b79cf000-b79d1000 rw-p 1000 08:04 > > 2747181/lib/tls/i686/cmov/libdl-2.6.1.so > > b79d1000-b79d5000 r-xp 08:04 > > 2486327/usr/lib/libXdmcp.so.6.0.0 > > b79d5000-b79d6000 rw-p 3000 08:04 > > 2486327/usr/lib/libXdmcp.so.6.0.0 > > b79d6000-b79d8000 r-xp 08:04 > > 2485527/usr/lib/libXau.so.6.0.0 > > b79d8000-b79d9000 rw-p 1000 08:04 > > 2485527/usr/lib/libXau.so.6.0.0 > > b79d9000-b79da000 rw-p b79d9000 00:00 0 > > b79da000-b7b1e000 r-xp 08:04 > > 2747161/lib/tls/i686/cmov/libc-2.6.1.so > > b7b1e000-b7b1f000 r--p 00143000 08:04 > > 2747161/lib/tls/i686/cmov/libc-2.6.1.so > > b7b1f000-b7b21000 rw-p 00144000 08:04 > > 2747161/lib/tls/i686/cmov/libc-2.6.1.so > > b7b21000-b7b24000 rw-p b7b21000 00:00 0 > > b7b24000-b7c11000 r-xp 08:04 > > 2486347/usr/lib/libX11.so.6.2.0 > > b7c11000-b7c15000 rw-p 000ed000 08:04 > > 2486347/usr/lib/libX11.so.6.2.0 > > b7c15000-b7c2a000 r-xp 08:04 > > 2488182/usr/lib/libICE.so.6.3.0 > > b7c2a000-b7c2c000 rw-p 00014000 08:04 > > 2488182/usr/lib/libICE.so.6.3.0 > > b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 > > b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 > > b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 > > b7c35000-b7c58000 r-xp 08:04 > > 2747187/lib/tls/i686/cmov/libm-2.6.1.so > > b7c58000-b7c5a000 rw-p 00023000 08:04 > > 2747187/lib/tls/i686/cmov/libm-2.6.1.so > > b7c5a000-b7c6e000 r-xp 08:04 > > 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so > > b7c6e000-b7c7 rw-p 00013000 08:04 > > 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so > > b7c7-b7c73000 rw-p b7c7 00:00 0 > > b7c73000-b7e27000 r-xp 08:04 > > 2491023/usr/lib/libgmx.so.4.0.0 > > b7e27000-b7e3 rw-p 001b3000 08:04 > > 2491023/usr/lib/libgmx.so.4.0.0 > > b7e3-b7e35000 rw-p b7e3 00:00 0 > > b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 > > b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 > > b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 > > b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 > > b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 > > b7f59000-b7f5c000 rw-p b7f59000 00:00 0 > > b7f5c000-b7f76000 r-xp 08:04 2747274/lib/ld-2.6.1.so > > b7f76000-b7f78000 rw-p 00019000 08:04 2747274/lib/ld-2.6.1.so > > bfa98000-bfaad000 rwxp bfa98000 00:00 0 [stack] > > bfaad000-bfaae000 rw-p bfaad000 00:00 0 > > e000-f000 r-xp 00:00 0
Re: [gmx-users] can not pass gmxtest
Hi, You shall always try to build gromacs yourself. What's the error with tutorial? Regards, Yang Ye On 11/7/2007 10:14 AM, Li Qiang wrote: hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp 08:04 2747274/lib/ld-2.6.1.so b7f76000-b7f78000 rw-p 00019000 08:04 2747274/lib/ld-2.6.1.so bfa98000-bfaad000 rwxp bfa98000 00:00 0 [stack] bfaad000-bfaae000 rw-p bfaad000 00:00 0 e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] can not pass gmxtest
> hi all, > > I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package > Manager(SPM). However, it can not pass the gamxtest with log as below, > but Tutorials seems OK. > Actually I try to compile myself at the beginning. It is weird that the > self-compiled one can pass the test but failed to run Tutorials with > Segmental fault at PR MD step. So probably you've done something weird to your environment in the meantime :-) > Does anyboby know how to solve it? and how to uninstall GROMACS clear? >From Synaptic, ask them. From source install, "make uninstall" Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] can not pass gmxtest
hi all, I newly installed GROMACS on UBUNTU 7.10 from Synaptic Package Manager(SPM). However, it can not pass the gamxtest with log as below, but Tutorials seems OK. Actually I try to compile myself at the beginning. It is weird that the self-compiled one can pass the test but failed to run Tutorials with Segmental fault at PR MD step. Does anyboby know how to solve it? and how to uninstall GROMACS clear? thanks a lot. output from gmxtest: ++ *** glibc detected *** mdrun: realloc(): invalid next size: 0x08076ec8 *** === Backtrace: = /lib/tls/i686/cmov/libc.so.6[0xb7a45b0c] /lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7a47a66] /usr/lib/libgmx.so.4(save_realloc+0x39)[0xb7cbe439] /usr/lib/libgmx.so.4(mk_graph+0x494)[0xb7cadde4] mdrun[0x8059f50] mdrun[0x805a72a] /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb79f0050] mdrun[0x804a491] === Memory map: 08048000-08062000 r-xp 08:04 2490502/usr/bin/mdrun 08062000-08063000 rw-p 00019000 08:04 2490502/usr/bin/mdrun 08063000-08085000 rw-p 08063000 00:00 0 [heap] b780-b7821000 rw-p b780 00:00 0 b7821000-b790 ---p b7821000 00:00 0 b79cc000-b79cd000 rw-p b79cc000 00:00 0 b79cd000-b79cf000 r-xp 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79cf000-b79d1000 rw-p 1000 08:04 2747181/lib/tls/i686/cmov/libdl-2.6.1.so b79d1000-b79d5000 r-xp 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d5000-b79d6000 rw-p 3000 08:04 2486327/usr/lib/libXdmcp.so.6.0.0 b79d6000-b79d8000 r-xp 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d8000-b79d9000 rw-p 1000 08:04 2485527/usr/lib/libXau.so.6.0.0 b79d9000-b79da000 rw-p b79d9000 00:00 0 b79da000-b7b1e000 r-xp 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1e000-b7b1f000 r--p 00143000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b1f000-b7b21000 rw-p 00144000 08:04 2747161/lib/tls/i686/cmov/libc-2.6.1.so b7b21000-b7b24000 rw-p b7b21000 00:00 0 b7b24000-b7c11000 r-xp 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c11000-b7c15000 rw-p 000ed000 08:04 2486347/usr/lib/libX11.so.6.2.0 b7c15000-b7c2a000 r-xp 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2a000-b7c2c000 rw-p 00014000 08:04 2488182/usr/lib/libICE.so.6.3.0 b7c2c000-b7c2d000 rw-p b7c2c000 00:00 0 b7c2d000-b7c34000 r-xp 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c34000-b7c35000 rw-p 6000 08:04 2487000/usr/lib/libSM.so.6.0.0 b7c35000-b7c58000 r-xp 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c58000-b7c5a000 rw-p 00023000 08:04 2747187/lib/tls/i686/cmov/libm-2.6.1.so b7c5a000-b7c6e000 r-xp 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c6e000-b7c7 rw-p 00013000 08:04 2747206/lib/tls/i686/cmov/libnsl-2.6.1.so b7c7-b7c73000 rw-p b7c7 00:00 0 b7c73000-b7e27000 r-xp 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e27000-b7e3 rw-p 001b3000 08:04 2491023/usr/lib/libgmx.so.4.0.0 b7e3-b7e35000 rw-p b7e3 00:00 0 b7e35000-b7f4a000 r-xp 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4a000-b7f4b000 rw-p 00114000 08:04 2491025/usr/lib/libmd.so.4.0.0 b7f4b000-b7f4c000 rw-p b7f4b000 00:00 0 b7f4e000-b7f58000 r-xp 08:04 2747267/lib/libgcc_s.so.1 b7f58000-b7f59000 rw-p a000 08:04 2747267/lib/libgcc_s.so.1 b7f59000-b7f5c000 rw-p b7f59000 00:00 0 b7f5c000-b7f76000 r-xp 08:04 2747274/lib/ld-2.6.1.so b7f76000-b7f78000 rw-p 00019000 08:04 2747274/lib/ld-2.6.1.so bfa98000-bfaad000 rwxp bfa98000 00:00 0 [stack] bfaad000-bfaae000 rw-p bfaad000 00:00 0 e000-f000 r-xp 00:00 0 [vdso] FAILED. Check files in rb1 1 out of 16 simple tests FAILED FAILED. Check files in acetonitrilRF FAILED. Check files in dec+water 2 out of 14 complex tests FAILED All 63 kernel tests PASSED All 45 pdb2gmx tests PASSED ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
