<div dir="ltr"><p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Dear Prof. Peter
Blaha and WIEN2k users,</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">Thank you. Now my
.machines file is:</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(31,73,125)">lapw0:e0591:4</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(31,73,125)">1:e0591:4</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(31,73,125)">1:e0591:4</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(31,73,125)">granularity:1</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(31,73,125)">extrafine:1</span></p>
<p class="MsoNormal" style="line-height:12.65pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial;margin:0cm 0cm 10pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;font-family:"Times New Roman",serif">I have installed WIEN2k
in my user in the cluster. When I use this script “</span><span style="font-size:12pt;font-family:"Times New Roman",serif;color:rgb(31,73,125)">srun --pty /bin/bash” </span><span style="font-size:12pt;font-family:"Times New Roman",serif">then it goes to one node of the cluster, the “<span style="color:rgb(31,73,125)">ls -als $WIENROOT/lapw0</span>”, “<span style="color:rgb(31,73,125)">x lapw0</span>” and “<span style="color:rgb(31,73,125)">lapw0 lapw0.def</span>” commands are
executed but, “<span style="color:rgb(31,73,125)">x lapw0 –p</span>”
is not executed.</span><span style="font-size:12pt;font-family:"Times New Roman",serif"> The following error appears:</span><span style="font-size:12pt;font-family:"Times New Roman",serif"></span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">There
are not enough slots available in the system to satisfy the 4</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">slots
that were requested by the application:</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> /home/users/mollabashi/v19.2/lapw0_mpi</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">Either
request fewer slots for your application, or make more slots</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">available
for use.</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">A
"slot" is the Open MPI term for an allocatable unit where we can</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">launch
a process. The number of slots available
are defined by the</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">environment
in which Open MPI processes are run:</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> 1. Hostfile, via "slots=N" clauses
(N defaults to number of</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> processor cores if not provided)</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> 2. The --host command line parameter, via a
":N" suffix on the</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> hostname (N defaults to 1 if not provided)</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> 3. Resource manager (e.g., SLURM, PBS/Torque,
LSF, etc.)</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> 4. If none of a hostfile, the --host command
line parameter, or an</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"> RM is present, Open MPI defaults to the
number of processor cores</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">In
all the above cases, if you want Open MPI to default to the number</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">of
hardware threads instead of the number of processor cores, use the</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">--use-hwthread-cpus
option.</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">Alternatively,
you can use the --oversubscribe option to ignore the</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">number
of available slots when deciding the number of processes to</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">launch.</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">--------------------------------------------------------------------------</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">[1] Exit 1 mpirun -np 4
-machinefile .machine0 /home/users/mollabashi/v19.2/lapw0_mpi lapw0.def
>> .time00</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">0.067u
0.091s 0:02.97 5.0% 0+0k 52272+144io
54pf+0w</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)">mollabashi@eagle:~/test1/cein$
cat .machines</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:black">Sincerely yours,</span></p>
<p class="MsoNormal" style="margin:0cm 0cm 10pt;line-height:115%;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:black">Leila Mollabashi</span><span style="font-size:12pt;line-height:115%;font-family:"Times New Roman",serif;color:rgb(31,73,125)"></span></p></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Apr 11, 2021 at 9:40 PM Peter Blaha <<a href="mailto:pblaha@theochem.tuwien.ac.at">pblaha@theochem.tuwien.ac.at</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Your script is still wrong.<br>
The .machines file should show:<br>
<br>
lapw0:e0150:4<br>
<br>
not<br>
lapw0:e0150<br>
:4<br>
<br>
Therefore it tries to execute lapw0 instead of lapw0_mpi.<br>
-----------<br>
Anyway, the first thing is to make the sequential wien2k running. You <br>
claimed the WIENROOT is known in the batch job.<br>
Please do:<br>
ls -als $WIENROOT/lapw0<br>
<br>
Does it have execute permission ?<br>
<br>
If yes, execute lapw0 explicitly:<br>
<br>
x lapw0<br>
<br>
and a second time:<br>
<br>
lapw0 lapw0.def<br>
<br>
<br>
Am 11.04.2021 um 13:17 schrieb leila mollabashi:<br>
> Dear Prof. Peter Blaha,<br>
> <br>
> Thank you for your guides. You are right. I edited the script and added <br>
> “source ~/.bashrc, echo 'lapw0:'`hostname`' :'$nproc >> .machines” to it.<br>
> <br>
> The crated .machines file is as follows:<br>
> <br>
> lapw0:e0150<br>
> <br>
> :4<br>
> <br>
> 1:e0150:4<br>
> <br>
> 1:e0150:4<br>
> <br>
> granularity:1<br>
> <br>
> extrafine:1<br>
> <br>
> The slurm.out file is:<br>
> <br>
> e0150<br>
> <br>
> # .machines<br>
> <br>
> bash: lapw0: command not found<br>
> <br>
> real 0m0.001s<br>
> <br>
> user 0m0.001s<br>
> <br>
> sys 0m0.000s<br>
> <br>
> grep: *scf1*: No such file or directory<br>
> <br>
> grep: lapw2*.error: No such file or directory<br>
> <br>
>> stop error<br>
> <br>
> When I used the following commands:<br>
> <br>
> echo $WIENROOT<br>
> which lapw0<br>
> which lapw0_mpi<br>
> <br>
> The following paths were printed:<br>
> <br>
> /home/users/mollabashi/v19.2<br>
> <br>
> /home/users/mollabashi/v19.2/lapw0<br>
> <br>
> /home/users/mollabashi/v19.2/lapw0_mpi<br>
> <br>
> But the error is still exists:<br>
> <br>
> bash: lapw0: command not found<br>
> <br>
> When I used your script in (faq page), one time the .machines file was <br>
> generated.<br>
> <br>
> But it stopped due to an error.<br>
> <br>
> test.scf1_1: No such file or directory.<br>
> <br>
> grep: *scf1*: No such file or directory<br>
> <br>
> FERMI - Error<br>
> <br>
> When I loaded openmpi and ifort as well as icc in the script this error <br>
> appeared:<br>
> <br>
>>SLURM_NTASKS_PER_NODE: Undefined variable.<br>
> <br>
> Every time after that the<br>
> <br>
>>SLURM_NTASKS_PER_NODE: Undefined variable<br>
> <br>
> error happened when I used your scripts without changing it. I have <br>
> tried several times even in a new directory with no positive effect.<br>
> <br>
>>SLURM_NTASKS_PER_NODE: Undefined variable.<br>
> <br>
> Sincerely yours,<br>
> <br>
> Leila Mollabashi<br>
> <br>
> <br>
> _______________________________________________<br>
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> <br>
<br>
-- <br>
--------------------------------------------------------------------------<br>
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna<br>
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982<br>
Email: <a href="mailto:blaha@theochem.tuwien.ac.at" target="_blank">blaha@theochem.tuwien.ac.at</a> WIEN2k: <a href="http://www.wien2k.at" rel="noreferrer" target="_blank">http://www.wien2k.at</a><br>
WWW: <a href="http://www.imc.tuwien.ac.at" rel="noreferrer" target="_blank">http://www.imc.tuwien.ac.at</a><br>
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</blockquote></div>