April 2018 - Nek5000-users - mailman3.cels.anl.gov

Postpro, averages and fluctuations
by nek5000-users＠lists.mcs.anl.gov 18 Apr '18

18 Apr '18

Hi everyone, I've been collecting information in the mailing list about these topics, but I still have some doubts. After I finish my 3D simulations I'm interested in calculate the average field of u, v, w and T; and also the instantaneous fluctuation fields. Everything in a specific plane. So what I should do is to incorporate avg_all in usercheck, specifying a frequency as param(68). Then, when the simulation ends, I should run a case in postproc mode, that is setting nsteps=0, I should create a file with the averages filenames called case.list, and in usercheck call auto_averager. Is that going to create different files with the final averages? one for each field? Or is it going to load the results in nek and I should outpost them? Then, for the instantaneous fluctuations, I should load all my simulation results calling load_fld, and substrac them the average I just obtained, for each field. But I'm not sure how to do this. I read that when load_fld is called, the variables are set in vx, vy, vz, T, right? But since I have several case0.f000X files, then should I load them one by one, make the substract, outpost the fluctuation, and so on? Thank you very much in advance! Juan Pablo.

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dissipation rate
by nek5000-users＠lists.mcs.anl.gov 18 Apr '18

18 Apr '18

Hi Nek, Can anyone know how to interpolate the dissipation rate in nek? I think it should be similar with subroutine interp_v(uvw,xyz,n). But I dont know how to do in details. Kind reagrds, Jian

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Post-process in Matlab
by nek5000-users＠lists.mcs.anl.gov 17 Apr '18

17 Apr '18

Hi Neks, I have a 3D geometry that I want to post-process in Matlab. I saw the post <https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2016-November/003984.…> <https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2016-November/003976.…>Read Nek output in Matlab <https://lists.mcs.anl.gov/mailman/htdig/nek5000-users/2016-November/003984.…> , but I’m not sure if it can post-process 3D data. Any help will be appreciated. The mesh consist of 22,000 elements N=7 Thanks Sula.

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dissipation rate
by nek5000-users＠lists.mcs.anl.gov 17 Apr '18

17 Apr '18

Hi Nek, Is there a subrountine in the nek I can get the turbulent dissipation rate in the position (x,y,z) which can have the similar interpolation function with interp_v below. subroutine interp_v(uvw,xyz,n) c c evaluate velocity for list of points xyz c include 'SIZE' include 'TOTAL' real uvw(ldim,n),xyz(ldim,n) parameter(nmax=lpart,nfldmx=ldim) common /rwk_intp/ $ fwrk(lx1*ly1*lz1*lelt,nfldmx), $ rwk(nmax,ldim+1), $ fpts(ldim*nmax), $ pts(ldim*nmax) common /iwk_intp/ $ iwk(nmax,3) integer icalld,e save icalld data icalld /0/ nxyz = nx1*ny1*nz1 ntot = nxyz*nelt if (n.gt.nmax) call exitti ('n > nmax in interp_v!$',n) if (nelgt.ne.nelgv) call exitti $ ('nelgt.ne.nelgv not yet supported in interp_v!$',nelgv) do i=1,n ! ? not moving -> save? pts(i) = xyz(1,i) pts(i + n) = xyz(2,i) if (if3d) pts(i + n*2) = xyz(3,i) enddo if (icalld.eq.0) then ! interpolation setup icalld = 1 tolin = 1.e-8 call intp_setup(tolin) endif ! pack working array call opcopy(fwrk(1,1),fwrk(1,2),fwrk(1,3),vx,vy,vz) ! interpolate call intp_do(fpts,fwrk,ndim, $ pts(1),pts(1+n),pts(2*n+1),n, $ iwk,rwk,nmax,.true.) do i=1,n uvw(1,i) = fpts(i) uvw(2,i) = fpts(i + n) if(if3d) uvw(3,i) = fpts(i + n*2) enddo return end Kind regards, Jian

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Re: [Nek5000-users] Problem on cluster
by nek5000-users＠lists.mcs.anl.gov 17 Apr '18

17 Apr '18

Amitvikram, yes, I'm using genmap correctly. I was able to solve the problem writing to the cluster administrators. They told me that I should send the batch from a directory where the flock flag is active. */mnt/flock*/mydirectory....... Thanks the answers! Juan Pablo.

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Problem on cluster
by nek5000-users＠lists.mcs.anl.gov 16 Apr '18

16 Apr '18

Dear Nek users, I'm having a problem when I use the latest version of Nek on a HPC cluster. I can compile, but when I run my simulations they finish. The logfile of a generic case is like the following: =========================================================== /----------------------------------------------------------\\ | _ __ ______ __ __ ______ ____ ____ ____ | | / | / // ____// //_/ / ____/ / __ \\/ __ \\/ __ \\ | | / |/ // __/ / ,< /___ \\ / / / // / / // / / / | | / /| // /___ / /| | ____/ / / /_/ // /_/ // /_/ / | | /_/ |_//_____//_/ |_|/_____/ \\___/ \\___/ \\___/ | | | |----------------------------------------------------------| | | | NEK5000: Open Source Spectral Element Solver | | COPYRIGHT (c) 2008-2017 UCHICAGO ARGONNE, LLC | | Version: 17.0-rc1 | | Web: http://nek5000.mcs.anl.gov | | | \\----------------------------------------------------------/ Number of processors: 80 REAL wdsize : 8 INTEGER wdsize : 4 Timer accuracy : 0.00E+00 Reading /home/jrobinson/casos/Placa_6/Placa_6.rea Reading /home/jrobinson/casos/Placa_6/Placa_6.re2 mapping elements to processors Reading /home/jrobinson/casos/Placa_6/Placa_6.ma2 RANK 0 IEG 1754 1755 1756 1757 1758 1759 1760 1774 1775 1776 1777 1778 1779 1780 1794 1795 1796 1797 1798 1799 1800 1814 1815 1816 1817 1818 1819 1820 1834 1835 1836 1837 1838 1839 1840 1853 1854 1855 1856 1857 1858 1859 1860 1873 1874 1875 1876 1877 1878 1879 1880 1893 1894 1895 1896 1897 1898 1899 1913 1914 1915 1916 1917 1918 1919 1933 1934 1935 1936 1937 1938 1939 1953 1954 1955 1956 1957 1958 1974 1975 1976 1977 1978 1994 1995 1996 1997 1998 1999 2000 2014 2015 2016 2017 2018 2019 2020 9783 9784 9785 9786 9787 9788 9789 9790 9791 9792 9793 9794 9795 9796 9797 9798 9799 9800 9801 9802 9803 9804 9805 9806 9807 9808 9809 9810 9811 9812 9813 9814 9815 9816 9817 9818 9819 9820 9821 9822 9823 9824 9825 9826 9827 9828 9829 9830 9849 9855 9856 9861 9862 element load imbalance: 1 150 151 done :: mapping 0.32155 sec preading mesh ============================================================= So the last line is "preading mesh". This doesn't give too much information, but the cluster generates a file with the following errors (at the end of this text). When I use an old version of Nek on this same cluster, I have no problem running my cases. The problem is that I need to use the latest version because I'm using exo2nek routine for my meshes generated with Trelis (Cubit). Any idea of what could I do? Thank you all. Juan Pablo. ========================================================= This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 4A,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 84, length 10800 This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 11,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 32484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 3) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 11,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 86484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 8) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 14,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 248484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 23 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 23) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 108084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 10 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 10) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 10,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 259284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 24 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 24) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 118884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 11) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 14,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 140484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 13) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 10,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 280884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 26 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 26) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 151284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 14) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 14,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 291684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 27 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 27) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 162084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 15 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 15) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 10,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 302484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 28 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 28) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 172884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 16 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 16) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 10,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 324084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 30 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 30) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 334884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 21684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 345684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 32 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 32) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 43284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 356484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 33 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 33) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 11,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 54084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 5) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 367284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 34 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 34) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 64884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 6) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 378084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 35 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 35) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 75684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 388884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 36 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 36) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 97284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 9) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 12,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 421284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 39 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 39) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 129684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12) ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 216084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 20) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 183684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 17 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 17) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 226884, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 21 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 21) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd F,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 194484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 18 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 18) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 10,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 237684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 22) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 205284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 19 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 19) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 313284, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 29 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 29) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 11,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 10884, length 10800 This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 399684, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 37 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 37) application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1) This requires fcntl(2) to be implemented. As of 8/25/2011 it is not. Generic MPICH Message: File locking failed in ADIOI_Set_lock(fd 13,cmd F_SETLKW/7,type F_RDLCK/0,whence 0) with return value FFFFFFFF and errno 26. - If the file system is NFS, you need to use NFS version 3, ensure that the lockd daemon is running on all the machines, and mount the directory with the 'noac' option (no attribute caching). - If the file system is LUSTRE, ensure that the directory is mounted with the 'flock' option. ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 410484, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 38 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 38) slurmstepd: error: *** STEP 11073373.0 ON leftraru1 CANCELLED AT 2018-04-16T18:38:42 *** ADIOI_Set_lock:: Function not implemented ADIOI_Set_lock:offset 270084, length 10800 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 25 In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process 25) srun: Job step aborted: Waiting up to 32 seconds for job step to finish. srun: error: leftraru1: tasks 0-19: Killed srun: Terminating job step 11073373.0 srun: error: leftraru4: tasks 60-79: Killed srun: error: leftraru3: tasks 40-59: Killed srun: error: leftraru2: tasks 20-39: Killed

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Re: [Nek5000-users] Problem on cluster
by nek5000-users＠lists.mcs.anl.gov 16 Apr '18

16 Apr '18

Using the release or the master I have that problem. I'm guessing it is something I should tell to the adminstrators of the cluster, but I'm not sure what to say exactly. Juan Pablo.

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pipe flow with pressure gradient fixed
by nek5000-users＠lists.mcs.anl.gov 13 Apr '18

13 Apr '18

Hi nek, Further to last post. I tried the way in channel flow which seems like not woking since the velocity is lower. Best wishes, Zhai

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pipe flow with pressure gradient fixed
by nek5000-users＠lists.mcs.anl.gov 13 Apr '18

13 Apr '18

Hi nek, Is there a way to keep the pressure gradient in the usr file which can has the ability to simulate the single-phase pipe flow where para54 and para55 were kept at constant flow rate, let's take the single-phase pipe flow at Ret=360 as an example. Best wishes, Zhai

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Change boundary condition type with time?
by nek5000-users＠lists.mcs.anl.gov 13 Apr '18

13 Apr '18

Hi Neks, I wonder if it is possible to have boundary conditions that chage type with time? I want to simulate a flow where I make a 'puff' of fluid through a hole in a wall. After the puff is made it continues to evolve without beeing forced. Mathematically, this is what I want: 1. Dirichlet boundary conditions (ux,uy,uz) = (0,0,1) for the velocity at a part B of the boundary up to a time T. 2. Open boundary condition for the velocity at B for time > T. Is this possible to implement? Best, Johan

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