<div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>There must have been something wrong with the mpich install. I sort of cheated by re-compiling mpich using the amber mpich install helper script. (you essentially unpack the tarball into the AmberTools/src directory and then execute their install/config script) which installed mpich into the amber14/bin path. Then compiled dock6.mpi against that. When I then launched dock6.mpi It worked efficiently. Another sign that it worked was that it spawned the extra screen.out.# out files. </div><div><br></div><div><br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><span>
<br>
</span>Does your dock output file contain, eg:<br>
Parallel dock running 48 MPI processes<br>
?<br></blockquote><div><br></div><div>This was a very helpful clue, thank you Scott!</div><div><br></div><div>Oddly, the machine was indeed launching 48 dock6.mpi processes, but the log file and the calculations did not reflect that. </div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<br>
How many ligands are in the file specified by ligand_atom_file ?<br></blockquote><div><br></div><div>I was using 100 </div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
What happens when you run the mpi test:<br>
cd dock6/install/test; make parallel<br>
?<br>
<br></blockquote><div><br></div><div>I got:  </div><div><div>-bash-4.2$ make parallel</div><div>MPICH_HOME is defined to /home/jgough/dock6/mpich-install</div><div>cd mpi &amp;&amp; make test</div><div>make[1]: Entering directory `/home/jgough/dock6/install/test/mpi&#39;</div><div>make[2]: Entering directory `/home/jgough/dock6/install/test/mpi&#39;</div><div>cd ../grid_generation &amp;&amp; make test</div><div>make[3]: Entering directory `/home/jgough/dock6/install/test/grid_generation&#39;</div><div># Construct box to enclose spheres</div><div>../../../bin/showbox &lt; <a href="http://box.in" target="_blank">box.in</a> &gt; /dev/null</div><div>../dockdif box.pdb.save box.pdb</div><div>diffing box.pdb.save with box.pdb</div><div>PASSED</div><div>==============================================================</div><div># Compute scoring grids</div><div>../../../bin/grid -i <a href="http://grid.in" target="_blank">grid.in</a> -o grid.out</div><div>../dockdif grid.out.save grid.out</div><div>diffing grid.out.save with grid.out</div><div>PASSED</div><div>==============================================================</div><div>make[3]: Leaving directory `/home/jgough/dock6/install/test/grid_generation&#39;</div><div>make[2]: Leaving directory `/home/jgough/dock6/install/test/mpi&#39;</div><div>make[2]: Entering directory `/home/jgough/dock6/install/test/mpi&#39;</div><div><br></div><div>Processing parallel dock6 test mpi</div><div>/home/jgough/dock6/mpich-install/bin/mpirun -np 2 ../../../bin/dock6.mpi -i mpi.dockin -o mpi.dockmpiout</div><div>../dockdif -t 8 mpi.dockmpiout.save mpi.dockmpiout</div><div>diffing mpi.dockmpiout.save with mpi.dockmpiout</div><div>possible FAILURE:  check mpi.dockmpiout.dif</div><div>==============================================================</div><div>diffing mpi_ranked.mol2.save with mpi_ranked.mol2</div><div>PASSED</div><div>==============================================================</div><div>make[2]: Leaving directory `/home/jgough/dock6/install/test/mpi&#39;</div><div>make[1]: Leaving directory `/home/jgough/dock6/install/test/mpi&#39;</div></div><div><br></div><div>Contents of mpi.dockmpiout.dif:</div><div><br></div><div><div>6,7d5</div><div>&lt; Parallel dock running 2 MPI processes</div><div>&lt; --------------------------------------</div><div>102a101</div><div>&gt; ------------------------------------------------------------------------------------------</div><div>111a111,115</div><div>&gt; Molecule: ZINC00158442</div><div>&gt;  ERROR:  Could not complete growth.</div><div>&gt;          Confirm that the grid box is large enough to contain the ligand,</div><div>&gt;          and try increasing max_orientations.</div><div>&gt; -----------------------------------</div><div>200d203</div><div>&lt; Finalizing MPI Routines...</div></div><div><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
If you need more help then please send verbose and verbatim details.<br>
<span><font color="#888888"><br>
scott<br>
<br>
</font></span></blockquote></div><br></div></div>