<div dir="ltr">Hi,<div><br><div>Could you please help me, whenever I use the same files as that you used for the MSD, I am getting the segmentation fault as copied below and my cp2k version is the latest one, cp2k 6.1, I don't know why the segmentation fault for the already tested input files.</div><div><br></div><div><br></div><div><div>[hn1-srmhpc06:161286:0:161286] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil))</div><div>==== backtrace ====</div><div> 0 0x000000000067c69c __reftraj_util_MOD_compute_msd_reftraj() /home/rpillai/Libraries/cp2k-install/src/motion/reftraj_util.F:364</div><div> 1 0x0000000000777d0d __integrator_MOD_reftraj() /home/rpillai/Libraries/cp2k-install/src/motion/integrator.F:1629</div><div> 2 0x00000000006811f8 __velocity_verlet_control_MOD_velocity_verlet() /home/rpillai/Libraries/cp2k-install/src/motion/velocity_verlet_control.F:90</div><div> 3 0x000000000063b245 __md_run_MOD_qs_mol_dyn_low() /home/rpillai/Libraries/cp2k-install/src/motion/md_run.F:473</div><div> 4 0x000000000063bcd5 __md_run_MOD_qs_mol_dyn() /home/rpillai/Libraries/cp2k-install/src/motion/md_run.F:152</div><div> 5 0x00000000004ea237 __cp2k_runs_MOD_cp2k_run() /home/rpillai/Libraries/cp2k-install/src/start/cp2k_runs.F:356</div><div> 6 0x00000000004ed4c2 __cp2k_runs_MOD_run_input() /home/rpillai/Libraries/cp2k-install/src/start/cp2k_runs.F:1103</div><div> 7 0x00000000004e70db MAIN__() /home/rpillai/Libraries/cp2k-install/src/start/cp2k.F:281</div><div> 8 0x000000000043a3bd main() /home/rpillai/Libraries/cp2k-install/obj/local/popt/cp2k.F90:45</div><div> 9 0x0000000000022445 __libc_start_main() ???:0</div><div>10 0x00000000004e695c _start() ???:0</div><div>===================</div><div>Segmentation fault (core dumped)</div></div><div><br></div><div><br></div><div><br></div><div><div><br></div><div> CP2K| version string: CP2K version 6.1</div><div> CP2K| source code revision number: svn:18464</div><div> CP2K| cp2kflags: libint fftw3 libxc parallel mpi3 scalapack xsmm libderiv_max_a</div><div> CP2K| m1=5 libint_max_am=6</div><div> CP2K| is freely available from https://www.cp2k.org/</div><div> CP2K| Program compiled at Wed Jul 3 15:39:08 IST 2019</div><div> CP2K| Program compiled on hn1-srmhpc06</div><div> CP2K| Program compiled for local</div><div> CP2K| Data directory path /home/rpillai/Libraries/cp2k-install/data</div><div> CP2K| Input file name runtime_cp2k.inp</div><div><br></div><div><br></div><div>Thanks in advance</div><div>renjith</div><div><br></div><br>On Monday, August 10, 2015 at 3:25:04 PM UTC+5:30, Marcella Iannuzzi wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;"><div dir="ltr">Hi Johannes<div><br></div><div>I tried your input and it runs fine, I did not get any segmentation fault.</div><div>As expected two output files are written, one per kind, with the MSD </div><div>For kind 2:</div><div><p style="font-size:12px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> 0 0.000 0.0000000000 0.0000000000 0.0000000000 0.0000000000</p>
<p style="font-size:12px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> 1 1.000 0.0000202689 0.0000306356 0.0000178320 0.0000687364</p>
<p style="font-size:12px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> 2 2.000 0.0000739085 0.0001240880 0.0000741001 0.0002720966</p>
<p style="font-size:12px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> 3 3.000 0.0001532087 0.0002815130 0.0001712799 0.0006060016</p>
<p style="font-size:12px;font-family:'Andale Mono';color:rgb(41,249,20);background-color:rgb(0,0,0)"> 4 4.000 0.0002589779 0.0005096011 0.0003126593 0.0010812382</p><div><br></div><div>Kind regards</div><div>Marcella</div><div><br></div><br>On Monday, August 3, 2015 at 4:08:09 PM UTC+2, Johannes Wagner wrote:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><br><br>Here are my input files:<br><br>runtime_cp2k is the main input<br>ref0.xy contains the reference coordinates<br><a href="http://reftraj.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Freftraj.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw-C-8a-NYuJOtEsmq017zKqRYKw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Freftraj.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGw-C-8a-NYuJOtEsmq017zKqRYKw';return true;">reftraj.xyz</a> contains the trajectory from a previous run.<br><br>all I get is a segmentation fault and I am not sure where to look for the error..<br><br><br>Am Montag, 3. August 2015 14:22:33 UTC+2 schrieb Johannes Wagner:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi Marcella,<br><br>I figured that, finding<br>REF0_FILENAME <br>under &MSD<br><br>however the error remains the same.<br>What format do both, the REF0 and the trajectory, need to have? both are XMOL in my case, one containing the entire trajectory, the other only the first step<br>like this <br><br><a href="http://ref0.xyz" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fref0.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFhh8SIFKvGf7bOMiiOkmHTatL6Xg';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fref0.xyz\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNFhh8SIFKvGf7bOMiiOkmHTatL6Xg';return true;">ref0.xyz</a><br> Cryst x<br> i = 0, time = 0.000, E = -16.1066791009<br> O 4.4494725764 0.8609855793 6.0981987308<br> O 3.8029095709 2.7229831166 4.5699381898<br> O 4.0118989226 2.7023681308 1.2194938263<br> O 6.0462348498 3.2953089592 5.9203028333<br> O 3.2241009956 5.5031225318 4.3400008035<br>..<br>..<br><br><br><br><br>Am Montag, 3. August 2015 11:23:12 UTC+2 schrieb Marcella Iannuzzi:<blockquote class="gmail_quote" style="margin:0;margin-left:0.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi<p>The MSD calculation with REFTRAJ needs a <br>Reference coordinates file</p><p>Regards</p><p>Marcella </p><p></p><p></p></blockquote></div></blockquote></div></blockquote></div></div></blockquote></div></div></div>