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.
[1] e.g. https://en.m.wikipedia.org/wiki/Out_of_memory _____ Professor Laurence Marks "Research is to see what everybody else has seen, and to think what nobody else has thought", Albert Szent-Gyorgi www.numis.northwestern.edu On Sun, Feb 23, 2020, 20:34 Gavin Abo <gs...@crimson.ua.edu> wrote: > 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. > > 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: > > /* Default unit number for preconnected standard input and output. */ > #define GFC_STDIN_UNIT_NUMBER 5 > #define GFC_STDOUT_UNIT_NUMBER 6 > #define GFC_STDERR_UNIT_NUMBER 0 > > However, as stated at [2]: > > *Like any other preconnected unit it may have its connection changed in an > open statement.* > > 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): > > open (iunit,file=fname,status=status,form=form) > > 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. > > 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. > > 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. > > *alloy_VOPT Calculation* > > username@computername:~/wiendata/alloy_VOPT$ ls > alloy_VOPT.struct > username@computername:~/wiendata/alloy_VOPT$ init_lapw -b > ... > username@computername:~/wiendata/alloy_VOPT$ gedit alloy_VOPT.in0 > username@computername:~/wiendata/alloy_VOPT$ cat alloy_VOPT.in0 > TOT XC_GGA_X_B86_R EC_LDA VC_LDA > (XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN) > NR2V IFFT (R2V) > 144 144 144 2.00 1 NCON 9 # min IFFT-parameters, enhancement > factor, iprint, NCON n > username@computername:~/wiendata/alloy_VOPT$ cp > $WIENROOT/SRC_templates/case.innlvdw alloy_VOPT.innlvdw > username@computername:~/wiendata/alloy_VOPT$ gedit alloy_VOPT.innlvdw > username@computername:~/wiendata/alloy_VOPT$ cat alloy_VOPT.innlvdw > 1 kernel type > -1.887 parameters of the kernel > 25 plane-wave expansion cutoff GMAX > 0.3 density cutoff rhoc > T calculation of the potential (T or F) > 10 plane-wave expansion cutoff GMAXpot for the potential > username@computername:~/wiendata/alloy_VOPT$ export > GFORTRAN_UNBUFFERED_ALL=1 > username@computername:~/wiendata/alloy_VOPT$ run_lapw -nlvdw > hup: Command not found. > grep: *scf1*: No such file or directory > grep: lapw2*.error: No such file or directory > > > stop error > username@computername:~/wiendata/alloy_VOPT$ cat alloy_VOPT.dayfile > > Calculating alloy_VOPT in /home/username/wiendata/alloy_VOPT > on computername with PID 26433 > using WIEN2k_19.1 (Release 25/6/2019) in /home/username/WIEN2k > > > start (Sun Feb 23 17:47:33 MST 2020) with nlvdw (40/99 to go) > > cycle 1 (Sun Feb 23 17:47:33 MST 2020) (40/99 to go) > > > nlvdw (17:47:33) Killed > 710.0u 58.6s 1:18:02.53 16.4% 0+0k 7490168+40io 262257pf+0w > error: command /home/username/WIEN2k/nlvdw nlvdw.def failed > > > stop error > username@computername:~/wiendata/alloy_VOPT$ cat alloy_VOPT.outputnlvdw > kernel type = 1 (M. Dion et al., PRL 92, 246401 (2004)) > parameter Z_ab of kernel = -1.88700000 > gmax = 25.0 > density cutoff rhoc = 0.300E+00 > the NL-vdW potential is calculated with gmax_pot = 10.0 > > n_max, m_max, p_max = 101 101 101 > ifft1, ifft2, ifft3 (for proc myid 0) = 203 203 203 > ifft1*ifft2*ifft3 (for proc myid 0) = 8365427 > Number of G-vectors (for proc myid 0) = 3099627 > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > % % > % You are using vdW-DF, which was implemented by the Thonhauser group. % > % Please cite the following two papers that made this development % > % possible and the two reviews that describe the various versions: % > % % > % T. Thonhauser et al., PRL 115, 136402 (2015). % > % T. Thonhauser et al., PRB 76, 125112 (2007). % > % K. Berland et al., Rep. Prog. Phys. 78, 066501 (2015). % > % D.C. Langreth et al., J. Phys.: Condens. Matter 21, 084203 (2009). % > % % > % % > % If you are calculating the stress with vdW-DF, please also cite: % > % % > % R. Sabatini et al., J. Phys.: Condens. Matter 24, 424209 (2012). % > % % > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > parameters of the kernel table: > Nq = 30, lambda = 0.111292E+01, q(1) = 0.100000E-04, q_cut = 0.100000E+02 > Nr_points = 2000, r_max = 100.0 > q_mesh = > 0.00001000 0.05312929 0.11224701 0.17804050 > 0.25126365 0.33275542 0.42344952 0.52438515 > 0.63671875 0.76173753 0.90087384 1.05572188 > 1.22805595 1.41985071 1.63330352 1.87086022 > 2.13524270 2.42948008 2.75694394 3.12138629 > 3.52698255 3.97838044 4.48075151 5.03985262 > 5.66208887 6.35459089 7.12529230 7.98302412 > 8.93761444 10.00000000 > > *Al Calculation* > > username@computername:~/wiendata/Al$ lsb_release -a > No LSB modules are available. > Distributor ID: Ubuntu > Description: Ubuntu 18.04.4 LTS > Release: 18.04 > Codename: bionic > username@computername:~/wiendata/Al$ cat $WIENROOT/WIEN2k_VERSION > WIEN2k_19.1 (Release 25/6/2019) > username@computername:~/wiendata/Al$ dpkg -l gfortran > Desired=Unknown/Install/Remove/Purge/Hold > | > Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend > |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) > ||/ Name Version Architecture Description > > +++-==============-============-============-================================= > ii gfortran 4:7.4.0-1ubu amd64 GNU Fortran 95 compiler > username@computername:~/wiendata/Al$ ls > Al.struct > username@computername:~/wiendata/Al$ init_lapw -b > ... > username@computername:~/wiendata/Al$ cp > $WIENROOT/SRC_templates/case.innlvdw Al.innlvdw > > For rev-vdW-DF2: > > username@computername:~/wiendata/Al$ cat Al.innldvdw > 1 kernel type > -1.887 parameters of the kernel > 25 plane-wave expansion cutoff GMAX > 0.3 density cutoff rhoc > T calculation of the potential (T or F) > 10 plane-wave expansion cutoff GMAXpot for the potential > username@computername:~/wiendata/Al$ cat Al.in0 > TOT XC_GGA_X_B86_R EC_LDA VC_LDA > (XC_LDA,XC_PBESOL,XC_WC,XC_MBJ,XC_SCAN) > NR2V IFFT (R2V) > 30 30 30 2.00 1 NCON 9 # min IFFT-parameters, enhancement > factor, iprint, NCON n > username@computername:~/wiendata/Al$ run_lapw -nlvdw > ... > in cycle 6 ETEST: .0003618600000000 CTEST: .0358926 > hup: Command not found. > STOP NLVDW END > STOP LAPW0 END > STOP LAPW1 END > STOP LAPW2 END > STOP CORE END > STOP MIXER END > ec cc and fc_conv 1 1 1 > > > stop > [1] http://mirrors.ocf.berkeley.edu/gnu/gcc/gcc-7.4.0/ > <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=> > [2] > https://stackoverflow.com/questions/44867775/fortran-code-wont-write-to-file > <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=> > [3] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19663.html > <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=> > [4] > https://stackoverflow.com/questions/1533717/how-do-i-flush-output-to-file-after-each-write-with-a-gfortran-fortran-90-progra > <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=> > [5] > https://gcc.gnu.org/onlinedocs/gcc-7.4.0/gfortran/GFORTRAN_005fUNBUFFERED_005fALL.html > <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=> > [6] > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg19667.html > <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=> > > > On 2/17/2020 3:16 AM, Peter Blaha wrote: > > But in nlvdw we do NOT write to the screen (except in case of some > errors). > > 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. > It should print all output on the screen then. > > > On 2/16/20 6:39 PM, Gavin Abo wrote: > > 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. > > > 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: > > > https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg16674.html > <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=> > > _______________________________________________ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > > https://urldefense.proofpoint.com/v2/url?u=http-3A__zeus.theochem.tuwien.ac.at_mailman_listinfo_wien&d=DwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=3ktO9qKFs01QXllahJ0fc5ALkn3_T6u6i1NdRT3bjfc&e= > SEARCH the MAILING-LIST at: > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_wien-40zeus.theochem.tuwien.ac.at_index.html&d=DwICAg&c=yHlS04HhBraes5BQ9ueu5zKhE7rtNXt_d012z2PA6ws&r=U_T4PL6jwANfAy4rnxTj8IUxm818jnvqKFdqWLwmqg0&m=2ndQWR6tn-8Au2xV9qWpEGZCDtC_VAKsykRUdroZfec&s=a5AHOSatTO1NiSyl3Z9dK2uczJXbUph24-zJzAqJGLI&e= >
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