<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>I installed gromacs 3.3.3 on Ubuntu Linux 9.10 running on a Intel(R) Core(TM)2 Quad CPU @ 2.40GHz w/ 4 GB RAM. I am getting the following errors for any of the gromacs commands, even when I am using the -h option to list the options available for that command. I removed the installation and installed a fresh copy of the 3.3.3 version. Then the commands work for a couple of times and again generates the same error of "buffer overflow" for all the subsequent tries once it starts throwing that error.</div><div><br></div><div>Then I tried to run the same simulation setup on another computer running AMD Phenom II running @ 3.00 GHz w/ 4 GB RAM and Gromacs 3.3.3. Everything runs without a hitch. </div><div><br></div><div>Below is a part of the error generated.</div><div>------------------------------</div><div><br></div><div>NNODES=4, MYRANK=0, HOSTNAME=xion<br>NNODES=4, MYRANK=1, HOSTNAME=xion<br>NNODES=4, MYRANK=3, HOSTNAME=xion<br>NNODES=4, MYRANK=2, HOSTNAME=xion<br>NODEID=1 argc=4<br>NODEID=0 argc=4<br>NODEID=3 argc=4<br>NODEID=2 argc=4<br> :-) G R O M A C S (-:<br><br>*** buffer overflow detected ***: mdrun_mpi terminated<br>======= Backtrace: =========<br>/lib/libc.so.6(__fortify_fail+0x37)[0x7f6bc65185f7]<br>/lib/libc.so.6[0x7f6bc65175a0]<br>/lib/libc.so.6[0x7f6bc6516457]<br>mdrun_mpi[0x4f7ea3]<br>mdrun_mpi[0x4f80da]<br>mdrun_mpi[0x4f8145]<br>mdrun_mpi[0x4e984a]<br>mdrun_mpi[0x4ea126]<br>mdrun_mpi[0x425d6c]<br>/lib/libc.so.6(__libc_start_main+0xfd)[0x7f6bc643fabd]<br>mdrun_mpi[0x403449]<br>======= Memory map: ========<br>00400000-0067f000 r-xp 00000000 08:01 2546 /usr/local/gromac<br>s/bin/mdrun_mpi<br>0087e000-0087f000 r-xp 0027e000 08:01 2546 /usr/local/gromac<br>s/bin/mdrun_mpi<br>0087f000-00887000 rwxp 0027f000 08:01 2546 /usr/local/gromac<br>s/bin/mdrun_mpi<br>00887000-0088d000 rwxp 00000000 00:00 0 <br>01b06000-01b2f000 rwxp 00000000 00:00 0 [heap]<br>7f6bc4bc8000-7f6bc4bde000 r-xp 00000000 08:01 7915 /lib/libgcc_s.so.<br>1<br><br></div><div>--------------------------------</div><div><br></div><div>Do you think there is some hardware issue?</div><div><br></div><div>Thanks any help regarding this is appreciated.</div><div><br></div><div>Venky</div><div><br><div>
<span class="Apple-style-span" style="font-size: 12px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: 'Calisto MT'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: 'Calisto MT'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: 'Calisto MT'; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Verdana; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</font></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">Venky Krishnamani</font></span></span></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">Dr.Janos K. Lanyi Lab,</font></span></span></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">D320, Medical Sciences I</font></span></span></div><div style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><span class="Apple-style-span" style="font-family: Verdana; font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">University of California, Irvine</font></span></span></div><font class="Apple-style-span" color="#7F7F7F">Irvine, CA 92697</font></span></span></span><div><font class="Apple-style-span" face="Verdana" size="3"><span class="Apple-style-span" style="font-size: 12px; "><font class="Apple-style-span" color="#7F7F7F">~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~</font></span></font></div></span></div></span>
</div>
<br></div></body></html>