<div dir="auto">Sounds like it was an OOM error [1]. There should be something in the system logs (e.g. /var/log). Since OOM handling is performed by the kernel it is not simple to trap this.<br><br>[1] e.g. <a href="https://en.m.wikipedia.org/wiki/Out_of_memory">https://en.m.wikipedia.org/wiki/Out_of_memory</a><br><div data-smartmail="gmail_signature">_____<br>Professor Laurence Marks<br>"Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi<br><a href="http://www.numis.northwestern.edu" target="_blank" rel="noreferrer">www.numis.northwestern.edu</a></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Feb 23, 2020, 20:34 Gavin Abo <<a href="mailto:gsabo@crimson.ua.edu" target="_blank" rel="noreferrer">gsabo@crimson.ua.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<p>I did some more testing of the nlvdw package compiled with
gfortran with .outputnlvdw having unit 6. A nlvdw calculation
runs fine. It does appear to just be due to a deficiency of
resources for my system. Further details given below should you
be interested in them.</p>
<p>In gcc-7.4.0.tar.gz at [1], it can be seen in
gcc/fortran/libgfortran.h that unit 6 and 5 are preconnected as
standard output and standard input, respectively, from:<br>
</p>
<p>/* Default unit number for preconnected standard input and
output. */<br>
#define GFC_STDIN_UNIT_NUMBER 5<br>
#define GFC_STDOUT_UNIT_NUMBER 6<br>
#define GFC_STDERR_UNIT_NUMBER 0<br>
</p>
<p>However, as stated at [2]:<br>
</p>
<p><i>Like any other preconnected unit it may have its connection
changed in an open statement.</i><br>
</p>
<p>Indeed, the preconnection of unit 6 as standard output is
overridden to write to the .outputnlvdw file instead by the open
statement in WIEN2k's SRC_nlvdw/vdw.F (on line 87 when iunit=6):<br>
</p>
<p> open (iunit,file=fname,status=status,form=form)<br>
</p>
<p>When I tried running Dr. Chakrabarti's alloy_VOPT.struct at [3]
with "run_lapw -nlvdw", the .dayfile gave me a "Killed" error and
.outputnlvdw was empty.</p>
<p>When I ran it, I found it strange that .outputnlvdw was empty.
It turned out that gfortran buffers file output in memory by
default such that the output was never written to the file when
the program was killed. I have found that the environmental
variable GFORTRAN_UNBUFFERED_ALL can be set to 1 [4]. Using
GFORTRAN_UNBUFFERED_ALL can slow down the small sequential reads
and writes [5] but is obviously better for debugging and also got
me passed what I previously reported that might be a gfortran bug
with buffered file output when using unit 6. As using a 'print
*,iunit' statement to try to debug the above open statement in
vdw.F printed to the .dayfile that files up to unit 5 were opened
but never showed unit 6 and the later files from nlvdw.def
opening.</p>
<p>The calculation I ran made it to the same spot as Dr. Chakrabarti
and expect the Ubuntu killed it due to insufficient RAM as Prof.
Tran pointed out at [6]. The small resource Al calculation ran
without errors though as shown below.<br>
</p>
<p><b>alloy_VOPT Calculation</b><br>
</p>
<p> <font color="#808080">username@computername:~/wiendata/alloy_VOPT$
ls<br>
alloy_VOPT.struct<br>
username@computername:~/wiendata/alloy_VOPT$ init_lapw -b<br>
...<br>
username@computername:~/wiendata/alloy_VOPT$ gedit
alloy_VOPT.in0<br>
username@computername:~/wiendata/alloy_VOPT$ cat alloy_VOPT.in0<br>
TOT XC_GGA_X_B86_R EC_LDA VC_LDA
(XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN)
<br>
NR2V IFFT (R2V)<br>
144 144 144 2.00 1 NCON 9 # min IFFT-parameters,
enhancement factor, iprint, NCON n<br>
username@computername:~/wiendata/alloy_VOPT$ cp
$WIENROOT/SRC_templates/case.innlvdw alloy_VOPT.innlvdw<br>
username@computername:~/wiendata/alloy_VOPT$ gedit
alloy_VOPT.innlvdw <br>
username@computername:~/wiendata/alloy_VOPT$ cat
alloy_VOPT.innlvdw <br>
1 kernel type<br>
-1.887 parameters of the kernel<br>
25 plane-wave expansion cutoff GMAX<br>
0.3 density cutoff rhoc<br>
T calculation of the potential (T or F)<br>
10 plane-wave expansion cutoff GMAXpot for the
potential<br>
username@computername:~/wiendata/alloy_VOPT$ export
GFORTRAN_UNBUFFERED_ALL=1<br>
username@computername:~/wiendata/alloy_VOPT$ run_lapw -nlvdw<br>
hup: Command not found.<br>
grep: *scf1*: No such file or directory<br>
grep: lapw2*.error: No such file or directory<br>
<br>
> stop error<br>
username@computername:~/wiendata/alloy_VOPT$ cat
alloy_VOPT.dayfile <br>
<br>
Calculating alloy_VOPT in /home/username/wiendata/alloy_VOPT<br>
on computername with PID 26433<br>
using WIEN2k_19.1 (Release 25/6/2019) in /home/username/WIEN2k<br>
<br>
<br>
start (Sun Feb 23 17:47:33 MST 2020) with nlvdw (40/99
to go)<br>
<br>
cycle 1 (Sun Feb 23 17:47:33 MST 2020) (40/99 to go)<br>
<br>
> nlvdw (17:47:33) Killed<br>
710.0u 58.6s 1:18:02.53 16.4% 0+0k 7490168+40io 262257pf+0w<br>
error: command /home/username/WIEN2k/nlvdw nlvdw.def failed<br>
<br>
> stop error<br>
username@computername:~/wiendata/alloy_VOPT$ cat
alloy_VOPT.outputnlvdw <br>
kernel type = 1 (M. Dion et al., PRL 92, 246401 (2004))<br>
parameter Z_ab of kernel = -1.88700000<br>
gmax = 25.0<br>
density cutoff rhoc = 0.300E+00<br>
the NL-vdW potential is calculated with gmax_pot = 10.0<br>
<br>
n_max, m_max, p_max = 101 101 101<br>
ifft1, ifft2, ifft3 (for proc myid 0) = 203 203 203<br>
ifft1*ifft2*ifft3 (for proc myid 0) = 8365427<br>
Number of G-vectors (for proc myid 0) = 3099627<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
% %<br>
% You are using vdW-DF, which was implemented by the Thonhauser
group. %<br>
% Please cite the following two papers that made this
development %<br>
% possible and the two reviews that describe the various
versions: %<br>
% %<br>
% T. Thonhauser et al., PRL 115, 136402
(2015). %<br>
% T. Thonhauser et al., PRB 76, 125112
(2007). %<br>
% K. Berland et al., Rep. Prog. Phys. 78, 066501
(2015). %<br>
% D.C. Langreth et al., J. Phys.: Condens. Matter 21, 084203
(2009). %<br>
% %<br>
% %<br>
% If you are calculating the stress with vdW-DF, please also
cite: %<br>
% %<br>
% R. Sabatini et al., J. Phys.: Condens. Matter 24, 424209
(2012). %<br>
% %<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
parameters of the kernel table:<br>
Nq = 30, lambda = 0.111292E+01, q(1) = 0.100000E-04, q_cut =
0.100000E+02<br>
Nr_points = 2000, r_max = 100.0<br>
q_mesh =<br>
0.00001000 0.05312929 0.11224701 0.17804050<br>
0.25126365 0.33275542 0.42344952 0.52438515<br>
0.63671875 0.76173753 0.90087384 1.05572188<br>
1.22805595 1.41985071 1.63330352 1.87086022<br>
2.13524270 2.42948008 2.75694394 3.12138629<br>
3.52698255 3.97838044 4.48075151 5.03985262<br>
5.66208887 6.35459089 7.12529230 7.98302412<br>
8.93761444 10.00000000</font><br>
</p>
<p><b>Al Calculation</b></p>
<p><font color="#808080">username@computername:~/wiendata/Al$
lsb_release -a<br>
No LSB modules are available.<br>
Distributor ID: Ubuntu<br>
Description: Ubuntu 18.04.4 LTS<br>
Release: 18.04<br>
Codename: bionic<br>
username@computername:~/wiendata/Al$ cat
$WIENROOT/WIEN2k_VERSION <br>
WIEN2k_19.1 (Release 25/6/2019)<br>
username@computername:~/wiendata/Al$ dpkg -l gfortran<br>
Desired=Unknown/Install/Remove/Purge/Hold<br>
|
Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend<br>
|/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad)<br>
||/ Name Version Architecture Description<br>
+++-==============-============-============-=================================<br>
ii gfortran 4:7.4.0-1ubu amd64 GNU Fortran 95
compiler<br>
username@computername:~/wiendata/Al$ ls<br>
Al.struct<br>
username@computername:~/wiendata/Al$ init_lapw -b<br>
...<br>
username@computername:~/wiendata/Al$ cp
$WIENROOT/SRC_templates/case.innlvdw Al.innlvdw<br>
<br>
For rev-vdW-DF2:<br>
<br>
username@computername:~/wiendata/Al$ cat Al.innldvdw <br>
1 kernel type<br>
-1.887 parameters of the kernel<br>
25 plane-wave expansion cutoff GMAX<br>
0.3 density cutoff rhoc<br>
T calculation of the potential (T or F)<br>
10 plane-wave expansion cutoff GMAXpot for the
potential<br>
username@computername:~/wiendata/Al$ cat Al.in0<br>
TOT XC_GGA_X_B86_R EC_LDA VC_LDA
(XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN)
<br>
NR2V IFFT (R2V)<br>
30 30 30 2.00 1 NCON 9 # min IFFT-parameters,
enhancement factor, iprint, NCON n<br>
username@computername:~/wiendata/Al$ run_lapw -nlvdw<br>
...<br>
in cycle 6 ETEST: .0003618600000000 CTEST: .0358926<br>
hup: Command not found.<br>
STOP NLVDW END<br>
STOP LAPW0 END<br>
STOP LAPW1 END<br>
STOP LAPW2 END<br>
STOP CORE END<br>
STOP MIXER END<br>
ec cc and fc_conv 1 1 1<br>
<br>
> stop</font><br>
</p>
[1] <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__mirrors.ocf.berkeley.edu_gnu_gcc_gcc-2D7.4.0_&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=eQjcCVoSqogB8I3gXkAPxUwcxtbS-Hm9O0xfNFd6WRs&e=" rel="noreferrer noreferrer" target="_blank">http://mirrors.ocf.berkeley.edu/gnu/gcc/gcc-7.4.0/</a><br>
[2]
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_44867775_fortran-2Dcode-2Dwont-2Dwrite-2Dto-2Dfile&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=8O22qnbrrW4on-g8vm9tQF3ZLIu6czlxzoALhypQAUw&e=" rel="noreferrer noreferrer" target="_blank">https://stackoverflow.com/questions/44867775/fortran-code-wont-write-to-file</a><br>
[3]
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_msg19663.html&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=Dy6-d-gkdrebvx4aGxrJPOUH4Lwr_YECpmw9N-j-i4c&e=" rel="noreferrer noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19663.html</a><br>
[4]
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__stackoverflow.com_questions_1533717_how-2Ddo-2Di-2Dflush-2Doutput-2Dto-2Dfile-2Dafter-2Deach-2Dwrite-2Dwith-2Da-2Dgfortran-2Dfortran-2D90-2Dprogra&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=HANLf_ggjL_sl0evR5wupdtim92P4VEV6F3C-fnDrYA&e=" rel="noreferrer noreferrer" target="_blank">https://stackoverflow.com/questions/1533717/how-do-i-flush-output-to-file-after-each-write-with-a-gfortran-fortran-90-progra</a><br>
[5]
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__gcc.gnu.org_onlinedocs_gcc-2D7.4.0_gfortran_GFORTRAN-5F005fUNBUFFERED-5F005fALL.html&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=Pr19bWzscoLNBm8DX_bG5L4qmVPcsjFI1Im6bSSzF5o&e=" rel="noreferrer noreferrer" target="_blank">https://gcc.gnu.org/onlinedocs/gcc-7.4.0/gfortran/GFORTRAN_005fUNBUFFERED_005fALL.html</a><br>
[6]
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_msg19667.html&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=AJaOsduDgoCJ_mlaxFFNZc592oqJQVEMBJuGnlQ9k0I&e=" rel="noreferrer noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19667.html</a>
<p><br>
</p>
<div>On 2/17/2020 3:16 AM, Peter Blaha
wrote:<br>
</div>
<blockquote type="cite">But
in nlvdw we do NOT write to the screen (except in case of some
errors).
<br>
<br>
In any case, please change nlvdw.def unit 6 to 66 and run nlvdw
nlved.def to verify if this is the source of the problem.
<br>
It should print all output on the screen then.
<br>
<br>
<br>
On 2/16/20 6:39 PM, Gavin Abo wrote:
<br>
<blockquote type="cite">Perhaps it's just my system but the WIEN2k
19.1 nlvdw, which has been compiled with gfortran (gcc version
7.4.0 under Ubuntu 18.04.4 LTS), is behaving strangely. It
seems to get hung up trying to open $file.outputnlvdw in
SCR_nlvdw/vdw.F. In x_lapw, I see $file.outputnlvdw defined as
unit 6.
<br>
<br>
<br>
It might be that use of unit 6 in the nlvdw package is
problematic when compiled with gfortran similar to what we saw
for SRC_symmetry:
<br>
<br>
<br>
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_msg16674.html&d=DwMD-g&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=ZpweoysBkNubrAwKeoEjwtQ2-CRv6cT5AF6PJ1Stqko&e=" rel="noreferrer noreferrer" target="_blank">https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16674.html</a><br>
</blockquote>
</blockquote>
</div>
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