From nek5000-users at lists.mcs.anl.gov Sun Jul 1 11:11:53 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Jul 2012 12:11:53 -0400 Subject: [Nek5000-users] Corrupt mesh In-Reply-To: References: Message-ID: Alex, Related question to Mani's. If one wanted to generate a box file explicitly giving the coordinates (as you suggested below), how should we span multiple lines in the .box file. If we needed 100 elements in the wall normal direction, for example, that wouldn't fit on a single line. I remember once trying to span multiple lines and genbox failed. Thanks, Josh On Sat, Jun 30, 2012 at 6:43 PM, wrote: > Hi Alex, > > Thank you for checking. > > Regards, > Mani > > > On 06/30/2012 05:24 AM, nek5000-users at lists.mcs.anl.gov wrote: >> >> Hi Mani, >> >> I got it -- you want to have boundary layers although it may be simpler >> just to give element coordinates explicitly in a single Box... >> >> Well, I generated .rea file from your .box file with repo version of >> genbox that looks fine in postx: >> >> http://www.mcs.anl.gov/~obabko/m1.tiff >> http://www.mcs.anl.gov/~obabko/m2.tiff >> >> Best. >> Aleks >> >> >> >> ----- Forwarded Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Friday, June 29, 2012 6:08:57 PM >> Subject: Re: [Nek5000-users] Corrupt mesh >> >> Hi Mani, >> >> I am curious what is a reason for not using a single Box instead of your >> current strategy of 27 Boxes with uniform element distribution: >> >> 1:-8 -8 -8 >> 2:-12 -8 -8 >> 3:-8 -8 -8 >> 4:-8 -12 -8 >> 5:-12 -12 -8 >> 6:-8 -12 -8 >> 7:-8 -8 -8 >> 8:-12 -8 -8 >> 9:-8 -8 -8 >> 10:-8 -8 -12 >> 11:-12 -8 -12 >> 12:-8 -8 -12 >> 13:-8 -12 -12 >> 14:-12 -12 -12 >> 15:-8 -12 -12 >> 16:-8 -8 -12 >> 17:-12 -8 -12 >> 18:-8 -8 -12 >> 19:-8 -8 -8 >> 20:-12 -8 -8 >> 21:-8 -8 -8 >> 22:-8 -12 -8 >> 23:-12 -12 -8 >> 24:-8 -12 -8 >> 25:-8 -8 -8 >> 26:-12 -8 -8 >> 27:-8 -8 -8 >> >> ? >> >> Thanks. >> Aleks >> >> >> >> ----- Original Message ----- >> From: nek5000-users at lists.mcs.anl.gov >> To: nek5000-users at lists.mcs.anl.gov >> Sent: Friday, June 29, 2012 4:43:46 PM >> Subject: [Nek5000-users] Corrupt mesh >> >> Dear Nek devs, >> >> I am using genbox to construct a mesh for a box of aspect ratio 1 x 1 x >> 1. But for some reason, the mesh seems to be corrupted, from what I see >> in VisIt (screenshot attached). I have attached the .box file used to >> construct this mesh. Could you help diagnose the reason for this error? >> >> Thanks, >> Mani >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -- Josh Camp "All that is necessary for the triumph of evil is that good men do nothing" -- Edmund Burke From nek5000-users at lists.mcs.anl.gov Sun Jul 1 15:29:55 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 1 Jul 2012 15:29:55 -0500 (CDT) Subject: [Nek5000-users] Corrupt mesh In-Reply-To: References: Message-ID: Just wrap to several lines, making them shorter than 80 characters Paul On Sun, 1 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Alex, > > Related question to Mani's. If one wanted to generate a box file > explicitly giving the coordinates (as you suggested below), how should > we span multiple lines in the .box file. If we needed 100 elements in > the wall normal direction, for example, that wouldn't fit on a single > line. I remember once trying to span multiple lines and genbox > failed. > > Thanks, > Josh > > On Sat, Jun 30, 2012 at 6:43 PM, wrote: >> Hi Alex, >> >> Thank you for checking. >> >> Regards, >> Mani >> >> >> On 06/30/2012 05:24 AM, nek5000-users at lists.mcs.anl.gov wrote: >>> >>> Hi Mani, >>> >>> I got it -- you want to have boundary layers although it may be simpler >>> just to give element coordinates explicitly in a single Box... >>> >>> Well, I generated .rea file from your .box file with repo version of >>> genbox that looks fine in postx: >>> >>> http://www.mcs.anl.gov/~obabko/m1.tiff >>> http://www.mcs.anl.gov/~obabko/m2.tiff >>> >>> Best. >>> Aleks >>> >>> >>> >>> ----- Forwarded Message ----- >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Sent: Friday, June 29, 2012 6:08:57 PM >>> Subject: Re: [Nek5000-users] Corrupt mesh >>> >>> Hi Mani, >>> >>> I am curious what is a reason for not using a single Box instead of your >>> current strategy of 27 Boxes with uniform element distribution: >>> >>> 1:-8 -8 -8 >>> 2:-12 -8 -8 >>> 3:-8 -8 -8 >>> 4:-8 -12 -8 >>> 5:-12 -12 -8 >>> 6:-8 -12 -8 >>> 7:-8 -8 -8 >>> 8:-12 -8 -8 >>> 9:-8 -8 -8 >>> 10:-8 -8 -12 >>> 11:-12 -8 -12 >>> 12:-8 -8 -12 >>> 13:-8 -12 -12 >>> 14:-12 -12 -12 >>> 15:-8 -12 -12 >>> 16:-8 -8 -12 >>> 17:-12 -8 -12 >>> 18:-8 -8 -12 >>> 19:-8 -8 -8 >>> 20:-12 -8 -8 >>> 21:-8 -8 -8 >>> 22:-8 -12 -8 >>> 23:-12 -12 -8 >>> 24:-8 -12 -8 >>> 25:-8 -8 -8 >>> 26:-12 -8 -8 >>> 27:-8 -8 -8 >>> >>> ? >>> >>> Thanks. >>> Aleks >>> >>> >>> >>> ----- Original Message ----- >>> From: nek5000-users at lists.mcs.anl.gov >>> To: nek5000-users at lists.mcs.anl.gov >>> Sent: Friday, June 29, 2012 4:43:46 PM >>> Subject: [Nek5000-users] Corrupt mesh >>> >>> Dear Nek devs, >>> >>> I am using genbox to construct a mesh for a box of aspect ratio 1 x 1 x >>> 1. But for some reason, the mesh seems to be corrupted, from what I see >>> in VisIt (screenshot attached). I have attached the .box file used to >>> construct this mesh. Could you help diagnose the reason for this error? >>> >>> Thanks, >>> Mani >>> >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > > -- > Josh Camp > > "All that is necessary for the triumph of evil is that good men do > nothing" -- Edmund Burke > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Jul 2 15:14:34 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 14:14:34 -0600 Subject: [Nek5000-users] Using postx In-Reply-To: Message-ID: Dear Nek5-heads I have run the example called turbChannel from the examples list and it seemed to run fine. However, when I try to look at the results using postx, I get the message "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" as the post-processor exits. I am also trying the do my own problem (a DNS in a square duct) using turbChannel as an example. But I can't look at my grid because I get the same message. What am I missing in the .rea file? Here is the turbChannel.rea file. Rich Johnson Idaho National Lab -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbChannel.rea Type: application/octet-stream Size: 4057 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 2 15:50:07 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 15:50:07 -0500 Subject: [Nek5000-users] Using postx In-Reply-To: References: Message-ID: Hi Rich, Right now, the current postx is looking for a specific number of logical flags, in a specific order within the .rea files. This will be changed soon, but for now, you can use the attached turbChannel.rea. For your own case, and until postnek is updated, the first 6 logical flags in the .rea must be: IFFLOW IFHEAT IFTRAN IFADVC IFCHAR IFAXIS For more info on each of these logical flags, please see the wiki: http://nek5000.mcs.anl.gov/index.php/LogicalSwitches Please let me know if that needs clarification. Thanks, Katie On Mon, Jul 2, 2012 at 3:14 PM, wrote: > > Dear Nek5-heads > > I have run the example called turbChannel from the examples list and it > seemed to run fine. However, when I try to look at the results using postx, > I get the message > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > as the post-processor exits. I am also trying the do my own problem (a > DNS in a square duct) using turbChannel as an example. But I can't look at > my grid because I get the same message. What am I missing in the .rea file? > > Here is the turbChannel.rea file. > > > > Rich Johnson > Idaho National Lab > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbChannel.rea Type: application/octet-stream Size: 4086 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 2 16:26:23 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 16:26:23 -0500 (CDT) Subject: [Nek5000-users] Using postx In-Reply-To: References: Message-ID: Hi Rich, Sorry about this. It turns out that most folks have been using VisIt for their analysis, so the incompatibility between postx and recent updates to file formats have generally not been an issue. I see from Katie's email that she's already working on an update to postx. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek5-heads > > I have run the example called turbChannel from the examples list and it > seemed to run fine. However, when I try to look at the results using > postx, I get the message > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > as the post-processor exits. I am also trying the do my own problem (a > DNS in a square duct) using turbChannel as an example. But I can't look at > my grid because I get the same message. What am I missing in the .rea > file? > > Here is the turbChannel.rea file. > > > > Rich Johnson > Idaho National Lab From nek5000-users at lists.mcs.anl.gov Mon Jul 2 16:44:18 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 15:44:18 -0600 Subject: [Nek5000-users] Using postx In-Reply-To: Message-ID: Hi Katie, I tried you suggestion and it still doesn't work and I did change the number of logical switches in the previous line and I did put them in order. Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/02/2012 02:50 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, Right now, the current postx is looking for a specific number of logical flags, in a specific order within the .rea files. This will be changed soon, but for now, you can use the attached turbChannel.rea. For your own case, and until postnek is updated, the first 6 logical flags in the .rea must be: IFFLOW IFHEAT IFTRAN IFADVC IFCHAR IFAXIS For more info on each of these logical flags, please see the wiki: http://nek5000.mcs.anl.gov/index.php/LogicalSwitches Please let me know if that needs clarification. Thanks, Katie On Mon, Jul 2, 2012 at 3:14 PM, wrote: Dear Nek5-heads I have run the example called turbChannel from the examples list and it seemed to run fine. However, when I try to look at the results using postx, I get the message "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" as the post-processor exits. I am also trying the do my own problem (a DNS in a square duct) using turbChannel as an example. But I can't look at my grid because I get the same message. What am I missing in the .rea file? Here is the turbChannel.rea file. Rich Johnson Idaho National Lab _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: turbChannel.rea Type: application/octet-stream Size: 4087 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 2 16:59:37 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 16:59:37 -0500 Subject: [Nek5000-users] svn issues? Message-ID: Howdy Neks, Having trouble checking out the latest svn - asking for username and password? -- Andrew Duggleby, Ph.D.,P.E., C.W.I. Assistant Professor Department of Mechanical Engineering Texas A&M University College Station, TX 77843-3123 109 Engineering Physics Building http://www1.mengr.tamu.edu/aduggleby (979) 862-7835 From nek5000-users at lists.mcs.anl.gov Mon Jul 2 17:09:34 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 17:09:34 -0500 Subject: [Nek5000-users] Using postx In-Reply-To: References: Message-ID: Hi Rich, Yes..it looks like there are several out of date issues with postx to be updated for the turbChannel case. I am working on an update now. Thanks Katie On Mon, Jul 2, 2012 at 4:44 PM, wrote: > > Hi Katie, > I tried you suggestion and it still doesn't work and I did change the > number of logical switches in the previous line and I did put them in order. > Rich > > > > *nek5000-users at lists.mcs.anl.gov* > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > > 07/02/2012 02:50 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > To > nek5000-users at lists.mcs.anl.gov > cc > Subject > Re: [Nek5000-users] Using postx > > > > > Hi Rich, > > Right now, the current postx is looking for a specific number of logical > flags, in a specific order within the .rea files. This will be changed > soon, but for now, you can use the attached turbChannel.rea. > > For your own case, and until postnek is updated, the first 6 logical flags > in the .rea must be: > > IFFLOW > IFHEAT > IFTRAN > IFADVC > IFCHAR > IFAXIS > > For more info on each of these logical flags, please see the wiki: * > http://nek5000.mcs.anl.gov/index.php/LogicalSwitches* > > Please let me know if that needs clarification. > Thanks, > Katie > > On Mon, Jul 2, 2012 at 3:14 PM, <*nek5000-users at lists.mcs.anl.gov*> > wrote: > > Dear Nek5-heads > > I have run the example called turbChannel from the examples list and it > seemed to run fine. However, when I try to look at the results using postx, > I get the message > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > as the post-processor exits. I am also trying the do my own problem (a > DNS in a square duct) using turbChannel as an example. But I can't look at > my grid because I get the same message. What am I missing in the .rea file? > > Here is the turbChannel.rea file. > > > > Rich Johnson > Idaho National Lab > _______________________________________________ > Nek5000-users mailing list* > **Nek5000-users at lists.mcs.anl.gov* * > **https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users* > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 2 17:12:16 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 17:12:16 -0500 (CDT) Subject: [Nek5000-users] svn issues? In-Reply-To: References: Message-ID: Hi Andrew, Thanks for the note. I just checked with mcs systems --- it seems to be a problem on their end and they're working on it. I'm guessing we'll be back online within 30-60 minutes. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Howdy Neks, > > Having trouble checking out the latest svn - asking for username and password? > > > -- > Andrew Duggleby, Ph.D.,P.E., C.W.I. > Assistant Professor > Department of Mechanical Engineering > Texas A&M University > College Station, TX 77843-3123 > > 109 Engineering Physics Building > http://www1.mengr.tamu.edu/aduggleby > (979) 862-7835 > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Jul 2 17:19:47 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 17:19:47 -0500 (CDT) Subject: [Nek5000-users] svn issues? In-Reply-To: References: Message-ID: Hi, I think it should now work. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Andrew, > > Thanks for the note. I just checked with mcs systems --- > it seems to be a problem on their end and they're working > on it. I'm guessing we'll be back online within 30-60 > minutes. > > Paul > > > On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Howdy Neks, >> >> Having trouble checking out the latest svn - asking for username and >> password? >> >> >> -- >> Andrew Duggleby, Ph.D.,P.E., C.W.I. >> Assistant Professor >> Department of Mechanical Engineering >> Texas A&M University >> College Station, TX 77843-3123 >> >> 109 Engineering Physics Building >> http://www1.mengr.tamu.edu/aduggleby >> (979) 862-7835 >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Jul 2 17:43:39 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 16:43:39 -0600 Subject: [Nek5000-users] Using postx In-Reply-To: Message-ID: Paul Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't read any of the files from nek5000. Do I need to set some switch to enable a visit file? Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/02/2012 03:27 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, Sorry about this. It turns out that most folks have been using VisIt for their analysis, so the incompatibility between postx and recent updates to file formats have generally not been an issue. I see from Katie's email that she's already working on an update to postx. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek5-heads > > I have run the example called turbChannel from the examples list and it > seemed to run fine. However, when I try to look at the results using > postx, I get the message > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > as the post-processor exits. I am also trying the do my own problem (a > DNS in a square duct) using turbChannel as an example. But I can't look at > my grid because I get the same message. What am I missing in the .rea > file? > > Here is the turbChannel.rea file. > > > > Rich Johnson > Idaho National Lab _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 2 18:00:19 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 18:00:19 -0500 (CDT) Subject: [Nek5000-users] Using postx In-Reply-To: References: Message-ID: Hi Rich, Great question -- I'm checking with Hank Childs to see if 2.4.0 is up to date with the Nek5000 reader. Also, I just noticed that the script we normally use to generate a meta-data file is not in the repo. It should be shortly -- it's called "nekvis". I usually use it (on linux platforms) by simply typing nekvis or nekvis session where session is the name of the .rea file. This script creates the metadata file and then launches VisIt. I'm attaching the script that I use here, but Katie is putting the latest into the repo. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Paul > Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't > read any of the files from nek5000. Do I need to set some switch to enable > a visit file? > Rich > > > > > nek5000-users at lists.mcs.anl.gov > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > 07/02/2012 03:27 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > > To > nek5000-users at lists.mcs.anl.gov > cc > > Subject > Re: [Nek5000-users] Using postx > > > > > > > > Hi Rich, > > Sorry about this. > > It turns out that most folks have been using VisIt for > their analysis, so the incompatibility between postx > and recent updates to file formats have generally not > been an issue. > > I see from Katie's email that she's already working on > an update to postx. > > Paul > > On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Nek5-heads >> >> I have run the example called turbChannel from the examples list and it >> seemed to run fine. However, when I try to look at the results using >> postx, I get the message >> "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" >> as the post-processor exits. I am also trying the do my own problem (a >> DNS in a square duct) using turbChannel as an example. But I can't look > at >> my grid because I get the same message. What am I missing in the .rea >> file? >> >> Here is the turbChannel.rea file. >> >> >> >> Rich Johnson >> Idaho National Lab > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- #! /bin/tcsh # # Shell script that generated VisIt metafile blah.nek5000 either from SESSION.NAME or from the first command line argument # set nfld = 0 # # of field files if ($#argv == 0) then if (-f SESSION.NAME) then set base = `head -1 SESSION.NAME` # case name else set nfld = -1 # exit echo echo ' No SESSION.NAME file -- Use "visnek case_name"' echo endif else set base = $argv[1] endif if ($nfld != -1) then echo echo ' Generating '$base'.nek5000 file ...' echo #echo 'endian little' > $base.nek5000 #echo 'endian big' > $base.nek5000 if (-e $base.fld01) then set nfld = `ls -1 $base{.fld[0-9][0-9]*} | wc -l` echo 'filetemplate: '$base'.fld%02d' > $base.nek5000 else if (-e 'A0/'$base'0.f00001') then set nfld = `ls -1 A0/$base{0.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: A%01d/'$base'%01d.f%05d' > $base.nek5000 else if (-e $base'00.f00001') then set nfld = `ls -1 $base{00.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: '$base'%02d.f%05d' > $base.nek5000 else if (-e 'A00/'$base'00.f00001') then set nfld = `ls -1 A00/$base{00.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: A%02d/'$base'%02d.f%05d' > $base.nek5000 else if (-e $base'000.f00001') then set nfld = `ls -1 $base{000.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: '$base'%03d.f%05d' > $base.nek5000 else if (-e 'A000/'$base'000.f00001') then set nfld = `ls -1 A000/$base{000.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: A%03d/'$base'%03d.f%05d' > $base.nek5000 else if (-e 'A0000/'$base'0000.f00001') then set nfld = `ls -1 A0000/$base{0000.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: A%04d/'$base'%04d.f%05d' > $base.nek5000 else set nfld = `ls -1 $base{0.f[0-9][0-9][0-9][0-9][0-9]} | wc -l` echo 'filetemplate: '$base'%01d.f%05d' > $base.nek5000 endif endif endif echo 'firsttimestep: 1' >> $base.nek5000 echo 'numtimesteps: '$nfld >> $base.nek5000 #echo 'meshcoords: 1' >> $base.nek5000 echo echo ' Assuming that coordinates are in the first file '$base'*.f*01 -- otherwise edit $base.nek5000 file ...' echo echo ' Also one may need to correct for an endian by inserting the first line "endian big" or "endian little" in case of, e.g., files transfered from other systems' echo echo echo ' Total '$nfld' file(s) are in the generated file '$base'.nek5000 ... Done!' echo endif # nfld != -1 visit -o $base.nek5000 From nek5000-users at lists.mcs.anl.gov Mon Jul 2 20:32:52 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 2 Jul 2012 18:32:52 -0700 Subject: [Nek5000-users] Using postx In-Reply-To: References: Message-ID: Hi Rich, You have to make a short header file that VisIt then opens. Aleks Obabko set up a how-to here: http://nek5000.mcs.anl.gov/index.php/VISIT#metata Aleks is gone, but I can help if you run into trouble. Just email me personally and we can get it figured out (hchilds at lbl.gov). Best, Hank On Mon, Jul 2, 2012 at 3:43 PM, wrote: > > Paul > Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't > read any of the files from nek5000. Do I need to set some switch to enable > a visit file? > Rich > > > > *nek5000-users at lists.mcs.anl.gov* > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > > 07/02/2012 03:27 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > To > nek5000-users at lists.mcs.anl.gov > cc > Subject > Re: [Nek5000-users] Using postx > > > > > > Hi Rich, > > Sorry about this. > > It turns out that most folks have been using VisIt for > their analysis, so the incompatibility between postx > and recent updates to file formats have generally not > been an issue. > > I see from Katie's email that she's already working on > an update to postx. > > Paul > > On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > > > Dear Nek5-heads > > > > I have run the example called turbChannel from the examples list and it > > seemed to run fine. However, when I try to look at the results using > > postx, I get the message > > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > > as the post-processor exits. I am also trying the do my own problem (a > > DNS in a square duct) using turbChannel as an example. But I can't look > at > > my grid because I get the same message. What am I missing in the .rea > > file? > > > > Here is the turbChannel.rea file. > > > > > > > > Rich Johnson > > Idaho National Lab > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Tue Jul 3 08:36:21 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Tue, 03 Jul 2012 15:36:21 +0200 Subject: [Nek5000-users] Velocity pressure coupling Message-ID: Hi, I am a new user of nek5000. With my colleagues, we are working on an improvement of the traction boundary condition in the pressure correction framework (as Goda scheme for instance). Analytical test have showed the efficiency of our proposal and now we would like to deal with physical test so we are very interested in nek5000. I would like to know how the velocity pressure coupling is ensured in nek5000 and in particular if pressure correction or velocity correction schemes are used?// //Thank you in advance. Etienne -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 5 11:46:53 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Jul 2012 10:46:53 -0600 Subject: [Nek5000-users] Using postx In-Reply-To: Message-ID: Okay, I made the header and got VisIt to read in a file. However, the spatial coordinates shown in VisIt are not correct. From the example menu, I use eddy_uv, a 2D problem that is defined on boundaries [0,1] for x and [0,1] for y. You can see this in the .box file and the .rea file. However, VisIt shows the domain as from [0,6.3] for both x and y, see attached figure. What is going on here? Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/02/2012 07:33 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, You have to make a short header file that VisIt then opens. Aleks Obabko set up a how-to here: http://nek5000.mcs.anl.gov/index.php/VISIT#metata Aleks is gone, but I can help if you run into trouble. Just email me personally and we can get it figured out (hchilds at lbl.gov). Best, Hank On Mon, Jul 2, 2012 at 3:43 PM, wrote: Paul Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't read any of the files from nek5000. Do I need to set some switch to enable a visit file? Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/02/2012 03:27 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, Sorry about this. It turns out that most folks have been using VisIt for their analysis, so the incompatibility between postx and recent updates to file formats have generally not been an issue. I see from Katie's email that she's already working on an update to postx. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek5-heads > > I have run the example called turbChannel from the examples list and it > seemed to run fine. However, when I try to look at the results using > postx, I get the message > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > as the post-processor exits. I am also trying the do my own problem (a > DNS in a square duct) using turbChannel as an example. But I can't look at > my grid because I get the same message. What am I missing in the .rea > file? > > Here is the turbChannel.rea file. > > > > Rich Johnson > Idaho National Lab _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eddy_uv.box Type: application/octet-stream Size: 288 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eddy_uv.rea Type: application/octet-stream Size: 131690 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: eddy_uv0000.png Type: application/octet-stream Size: 105753 bytes Desc: not available URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 5 12:50:32 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Jul 2012 12:50:32 -0500 (CDT) Subject: [Nek5000-users] Using postx In-Reply-To: Message-ID: Hi Rich, Please, read the header of the file eddy_uv.usr In this file geometry is remapped to 0 to 2 pi in usrdat2() Let me know if you have other questions. Aleks ----- Original Message ----- From: nek5000-users at lists.mcs.anl.gov To: nek5000-users at lists.mcs.anl.gov Sent: Thursday, July 5, 2012 11:46:53 AM Subject: Re: [Nek5000-users] Using postx Okay, I made the header and got VisIt to read in a file. However, the spatial coordinates shown in VisIt are not correct. From the example menu, I use eddy_uv, a 2D problem that is defined on boundaries [0,1] for x and [0,1] for y. You can see this in the .box file and the .rea file. However, VisIt shows the domain as from [0,6.3] for both x and y, see attached figure. What is going on here? Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/02/2012 07:33 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, You have to make a short header file that VisIt then opens. Aleks Obabko set up a how-to here: http://nek5000.mcs.anl.gov/index.php/VISIT#metata Aleks is gone, but I can help if you run into trouble. Just email me personally and we can get it figured out ( hchilds at lbl.gov ). Best, Hank On Mon, Jul 2, 2012 at 3:43 PM, < nek5000-users at lists.mcs.anl.gov > wrote: Paul Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't read any of the files from nek5000. Do I need to set some switch to enable a visit file? Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/02/2012 03:27 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, Sorry about this. It turns out that most folks have been using VisIt for their analysis, so the incompatibility between postx and recent updates to file formats have generally not been an issue. I see from Katie's email that she's already working on an update to postx. Paul On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek5-heads > > I have run the example called turbChannel from the examples list and it > seemed to run fine. However, when I try to look at the results using > postx, I get the message > "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" > as the post-processor exits. I am also trying the do my own problem (a > DNS in a square duct) using turbChannel as an example. But I can't look at > my grid because I get the same message. What am I missing in the .rea > file? > > Here is the turbChannel.rea file. > > > > Rich Johnson > Idaho National Lab _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Thu Jul 5 12:58:23 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Jul 2012 12:58:23 -0500 (CDT) Subject: [Nek5000-users] Using postx In-Reply-To: References: Message-ID: Hi Rich, This example is on [0,2pi]^2. Because it is a verification study for which we wish to test convergence, the geometry is rescaled in the .usr file (see routine usrdat) to get full 64-bit precision. If you go to: http://nek5000.mcs.anl.gov/index.php/UG#Documentation and click on Examples, you'll get a .pdf that describes the problem (p.6). Paul On Thu, 5 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Okay, I made the header and got VisIt to read in a file. However, the > spatial coordinates shown in VisIt are not correct. From the example menu, > I use eddy_uv, a 2D problem that is defined on boundaries [0,1] for x and > [0,1] for y. You can see this in the .box file and the .rea file. > However, VisIt shows the domain as from [0,6.3] for both x and y, see > attached figure. What is going on here? > Rich > > > > > > nek5000-users at lists.mcs.anl.gov > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > 07/02/2012 07:33 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > > To > nek5000-users at lists.mcs.anl.gov > cc > > Subject > Re: [Nek5000-users] Using postx > > > > > > > Hi Rich, > > You have to make a short header file that VisIt then opens. > > Aleks Obabko set up a how-to here: > http://nek5000.mcs.anl.gov/index.php/VISIT#metata > > Aleks is gone, but I can help if you run into trouble. Just email me > personally and we can get it figured out (hchilds at lbl.gov). > > Best, > Hank > > On Mon, Jul 2, 2012 at 3:43 PM, wrote: > > Paul > Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't > read any of the files from nek5000. Do I need to set some switch to enable > a visit file? > Rich > > > > > nek5000-users at lists.mcs.anl.gov > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > 07/02/2012 03:27 PM > > > Please respond to > nek5000-users at lists.mcs.anl.gov > > > To > nek5000-users at lists.mcs.anl.gov > cc > > Subject > Re: [Nek5000-users] Using postx > > > > > > > > > > Hi Rich, > > Sorry about this. > > It turns out that most folks have been using VisIt for > their analysis, so the incompatibility between postx > and recent updates to file formats have generally not > been an issue. > > I see from Katie's email that she's already working on > an update to postx. > > Paul > > On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Nek5-heads >> >> I have run the example called turbChannel from the examples list and it >> seemed to run fine. However, when I try to look at the results using >> postx, I get the message >> "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" >> as the post-processor exits. I am also trying the do my own problem (a >> DNS in a square duct) using turbChannel as an example. But I can't look > at >> my grid because I get the same message. What am I missing in the .rea >> file? >> >> Here is the turbChannel.rea file. >> >> >> >> Rich Johnson >> Idaho National Lab > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > From nek5000-users at lists.mcs.anl.gov Thu Jul 5 15:22:13 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 5 Jul 2012 14:22:13 -0600 Subject: [Nek5000-users] Using postx In-Reply-To: Message-ID: Thanks nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/05/2012 11:58 AM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using postx Hi Rich, This example is on [0,2pi]^2. Because it is a verification study for which we wish to test convergence, the geometry is rescaled in the .usr file (see routine usrdat) to get full 64-bit precision. If you go to: http://nek5000.mcs.anl.gov/index.php/UG#Documentation and click on Examples, you'll get a .pdf that describes the problem (p.6). Paul On Thu, 5 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Okay, I made the header and got VisIt to read in a file. However, the > spatial coordinates shown in VisIt are not correct. From the example menu, > I use eddy_uv, a 2D problem that is defined on boundaries [0,1] for x and > [0,1] for y. You can see this in the .box file and the .rea file. > However, VisIt shows the domain as from [0,6.3] for both x and y, see > attached figure. What is going on here? > Rich > > > > > > nek5000-users at lists.mcs.anl.gov > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > 07/02/2012 07:33 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > > To > nek5000-users at lists.mcs.anl.gov > cc > > Subject > Re: [Nek5000-users] Using postx > > > > > > > Hi Rich, > > You have to make a short header file that VisIt then opens. > > Aleks Obabko set up a how-to here: > http://nek5000.mcs.anl.gov/index.php/VISIT#metata > > Aleks is gone, but I can help if you run into trouble. Just email me > personally and we can get it figured out (hchilds at lbl.gov). > > Best, > Hank > > On Mon, Jul 2, 2012 at 3:43 PM, wrote: > > Paul > Okay, so how do I use VisIt. I have version 2.4.0 on my PC. But it won't > read any of the files from nek5000. Do I need to set some switch to enable > a visit file? > Rich > > > > > nek5000-users at lists.mcs.anl.gov > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > 07/02/2012 03:27 PM > > > Please respond to > nek5000-users at lists.mcs.anl.gov > > > To > nek5000-users at lists.mcs.anl.gov > cc > > Subject > Re: [Nek5000-users] Using postx > > > > > > > > > > Hi Rich, > > Sorry about this. > > It turns out that most folks have been using VisIt for > their analysis, so the incompatibility between postx > and recent updates to file formats have generally not > been an issue. > > I see from Katie's email that she's already working on > an update to postx. > > Paul > > On Mon, 2 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear Nek5-heads >> >> I have run the example called turbChannel from the examples list and it >> seemed to run fine. However, when I try to look at the results using >> postx, I get the message >> "PARAMETER DATA CORRUPTED OR MISSING FROM READ FILE" >> as the post-processor exits. I am also trying the do my own problem (a >> DNS in a square duct) using turbChannel as an example. But I can't look > at >> my grid because I get the same message. What am I missing in the .rea >> file? >> >> Here is the turbChannel.rea file. >> >> >> >> Rich Johnson >> Idaho National Lab > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Jul 8 06:30:47 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 8 Jul 2012 13:30:47 +0200 Subject: [Nek5000-users] Problem linking Prenek Message-ID: Dear all. I am new in Nek5000. I have been able to run the examples without any problem, and now I would like to build my mesh, so I would like to use Prenek. Everything compiles fine (I'm running ubuntu, and I have installed all the dependences) but when linking to the X11 it takes more than 4GB memory. I am building everything on my laptop and I don't know if it is usual to use that amount of RAM. If it is so, I will probably try on another computer. Can we also link the libraries dynamically? Regards -- Luis Parras Anguita Profesor Ayudante Doctor Departamento de Ing. Mec?nica y Mec?nica de Fluidos ETSII Industriales, M?laga. ----------------------------------------- Edificio de Ingenier?as C/ Arquitecto Francisco Pe?alosa S/N 29071 M?laga From nek5000-users at lists.mcs.anl.gov Sun Jul 8 06:59:26 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 8 Jul 2012 06:59:26 -0500 (CDT) Subject: [Nek5000-users] Problem linking Prenek In-Reply-To: References: Message-ID: Dear Luis, Edit the file tools/prenek/basics.inc and reduce "nelm" to, say, 10000. Then rebuild via maketools prenek This will reduce your memory footprint by 100x. Please let me know if other issues arise. Best regards, Paul Fischer On Sun, 8 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear all. > > I am new in Nek5000. I have been able to run the examples without any > problem, and now I would like to build my mesh, so I would like to use > Prenek. Everything compiles fine (I'm running ubuntu, and I have > installed all the dependences) but when linking to the X11 it takes > more than 4GB memory. I am building everything on my laptop and I > don't know if it is usual to use that amount of RAM. If it is so, I > will probably try on another computer. Can we also link the libraries > dynamically? > > Regards > > > -- > Luis Parras Anguita > Profesor Ayudante Doctor > Departamento de Ing. Mec?nica y Mec?nica de Fluidos > ETSII Industriales, M?laga. > ----------------------------------------- > Edificio de Ingenier?as > C/ Arquitecto Francisco Pe?alosa S/N > 29071 M?laga > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Jul 8 07:25:26 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 8 Jul 2012 14:25:26 +0200 Subject: [Nek5000-users] Problem linking Prenek In-Reply-To: References: Message-ID: Dear Paul... Works fine. Sorry for the question but I have searched the archive files of the users list I haven't found any problem like mine. Best regards 2012/7/8 : > > Dear Luis, > > Edit the file > > tools/prenek/basics.inc > > and reduce "nelm" to, say, 10000. Then rebuild via > > maketools prenek > > This will reduce your memory footprint by 100x. > > Please let me know if other issues arise. > > Best regards, > > Paul Fischer > > > > > On Sun, 8 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Dear all. >> >> I am new in Nek5000. I have been able to run the examples without any >> problem, and now I would like to build my mesh, so I would like to use >> Prenek. Everything compiles fine (I'm running ubuntu, and I have >> installed all the dependences) but when linking to the X11 it takes >> more than 4GB memory. I am building everything on my laptop and I >> don't know if it is usual to use that amount of RAM. If it is so, I >> will probably try on another computer. Can we also link the libraries >> dynamically? >> >> Regards >> >> >> -- >> Luis Parras Anguita >> Profesor Ayudante Doctor >> Departamento de Ing. Mec?nica y Mec?nica de Fluidos >> ETSII Industriales, M?laga. >> ----------------------------------------- >> Edificio de Ingenier?as >> C/ Arquitecto Francisco Pe?alosa S/N >> 29071 M?laga >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > -- Luis Parras Anguita Profesor Ayudante Doctor Departamento de Ing. Mec?nica y Mec?nica de Fluidos ETSII Industriales, M?laga. ----------------------------------------- Edificio de Ingenier?as C/ Arquitecto Francisco Pe?alosa S/N 29071 M?laga From nek5000-users at lists.mcs.anl.gov Sun Jul 8 07:27:30 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 8 Jul 2012 07:27:30 -0500 (CDT) Subject: [Nek5000-users] Problem linking Prenek In-Reply-To: References: Message-ID: Anytime. That's what the list is for! :) On Sun, 8 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Paul... > > Works fine. > > Sorry for the question but I have searched the archive files of the > users list I haven't found any problem like mine. > > Best regards > > 2012/7/8 : >> >> Dear Luis, >> >> Edit the file >> >> tools/prenek/basics.inc >> >> and reduce "nelm" to, say, 10000. Then rebuild via >> >> maketools prenek >> >> This will reduce your memory footprint by 100x. >> >> Please let me know if other issues arise. >> >> Best regards, >> >> Paul Fischer >> >> >> >> >> On Sun, 8 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Dear all. >>> >>> I am new in Nek5000. I have been able to run the examples without any >>> problem, and now I would like to build my mesh, so I would like to use >>> Prenek. Everything compiles fine (I'm running ubuntu, and I have >>> installed all the dependences) but when linking to the X11 it takes >>> more than 4GB memory. I am building everything on my laptop and I >>> don't know if it is usual to use that amount of RAM. If it is so, I >>> will probably try on another computer. Can we also link the libraries >>> dynamically? >>> >>> Regards >>> >>> >>> -- >>> Luis Parras Anguita >>> Profesor Ayudante Doctor >>> Departamento de Ing. Mec?nica y Mec?nica de Fluidos >>> ETSII Industriales, M?laga. >>> ----------------------------------------- >>> Edificio de Ingenier?as >>> C/ Arquitecto Francisco Pe?alosa S/N >>> 29071 M?laga >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > > -- > Luis Parras Anguita > Profesor Ayudante Doctor > Departamento de Ing. Mec?nica y Mec?nica de Fluidos > ETSII Industriales, M?laga. > ----------------------------------------- > Edificio de Ingenier?as > C/ Arquitecto Francisco Pe?alosa S/N > 29071 M?laga > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Mon Jul 9 17:21:23 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 16:21:23 -0600 Subject: [Nek5000-users] Using Visit In-Reply-To: Message-ID: Okay, So how do you ensure that the first field file has the mesh in it as required by VisIt? Rich Johnson -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 9 17:24:50 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 17:24:50 -0500 (CDT) Subject: [Nek5000-users] Using Visit In-Reply-To: References: Message-ID: Hi Rich, In principle, this happens automatically. Can you please do the following: head -1 blah | strings | head -1 where "blah" is the name of your first field file ? There should be an "X" in the header indicating that this has the geometry --- if not, I'd like to know about it so that we can fix whatever went wrong. Thanks, Paul On Mon, 9 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Okay, > So how do you ensure that the first field file has the mesh in it as > required by VisIt? > Rich Johnson > From nek5000-users at lists.mcs.anl.gov Mon Jul 9 17:31:09 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 16:31:09 -0600 Subject: [Nek5000-users] Using Visit In-Reply-To: Message-ID: Paul I issued your command and this is what I got. There is an X in there, but Visit doesn't think that the geometry is in there. (My square duct is 24 x 24 x 36 cells). Rich head -1 sqduct0.f00001 | strings | head -1 #std 4 8 8 8 20736 20736 0.1000000000000E-02 2 0 1 XUP nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/09/2012 04:25 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using Visit Hi Rich, In principle, this happens automatically. Can you please do the following: head -1 blah | strings | head -1 where "blah" is the name of your first field file ? There should be an "X" in the header indicating that this has the geometry --- if not, I'd like to know about it so that we can fix whatever went wrong. Thanks, Paul On Mon, 9 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Okay, > So how do you ensure that the first field file has the mesh in it as > required by VisIt? > Rich Johnson > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 9 17:41:23 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 15:41:23 -0700 Subject: [Nek5000-users] Using Visit In-Reply-To: References: Message-ID: Hi Rich, It sounds like the data is pretty small. Can you send sqduct0.f00001 and your .nek5000 file to hchilds at lbl.gov so I can take a look? Best, Hank On Mon, Jul 9, 2012 at 3:31 PM, wrote: > > Paul > > I issued your command and this is what I got. There is an X in there, but > Visit doesn't think that the geometry is in there. (My square duct is 24 x > 24 x 36 cells). > Rich > > head -1 sqduct0.f00001 | strings | head -1 > #std 4 8 8 8 20736 20736 0.1000000000000E-02 2 > 0 1 XUP > > > > *nek5000-users at lists.mcs.anl.gov* > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > > 07/09/2012 04:25 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > To > nek5000-users at lists.mcs.anl.gov > cc > Subject > Re: [Nek5000-users] Using Visit > > > > > > Hi Rich, > > In principle, this happens automatically. > > Can you please do the following: > > head -1 blah | strings | head -1 > > where "blah" is the name of your first field file ? > > There should be an "X" in the header indicating that this > has the geometry --- if not, I'd like to know about it so > that we can fix whatever went wrong. > > Thanks, > > Paul > > > On Mon, 9 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > > > Okay, > > So how do you ensure that the first field file has the mesh in it as > > required by VisIt? > > Rich Johnson > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 9 17:46:17 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 16:46:17 -0600 Subject: [Nek5000-users] Using Visit In-Reply-To: Message-ID: Hank The field file is 284 MB. I can try to send it via a large file method that we have here. Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/09/2012 04:41 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using Visit Hi Rich, It sounds like the data is pretty small. Can you send sqduct0.f00001 and your .nek5000 file to hchilds at lbl.gov so I can take a look? Best, Hank On Mon, Jul 9, 2012 at 3:31 PM, wrote: Paul I issued your command and this is what I got. There is an X in there, but Visit doesn't think that the geometry is in there. (My square duct is 24 x 24 x 36 cells). Rich head -1 sqduct0.f00001 | strings | head -1 #std 4 8 8 8 20736 20736 0.1000000000000E-02 2 0 1 XUP nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/09/2012 04:25 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using Visit Hi Rich, In principle, this happens automatically. Can you please do the following: head -1 blah | strings | head -1 where "blah" is the name of your first field file ? There should be an "X" in the header indicating that this has the geometry --- if not, I'd like to know about it so that we can fix whatever went wrong. Thanks, Paul On Mon, 9 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Okay, > So how do you ensure that the first field file has the mesh in it as > required by VisIt? > Rich Johnson > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 9 17:59:25 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 16:59:25 -0600 Subject: [Nek5000-users] Using Visit In-Reply-To: Message-ID: Hank I am having problems with my large file server. I will have to try again tomorrow. Do you still want me to send the file? I am wondering if the problem is that the mesh is too large. It worked okay for a much smaller mesh. Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/09/2012 04:47 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using Visit Hank The field file is 284 MB. I can try to send it via a large file method that we have here. Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/09/2012 04:41 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using Visit Hi Rich, It sounds like the data is pretty small. Can you send sqduct0.f00001 and your .nek5000 file to hchilds at lbl.gov so I can take a look? Best, Hank On Mon, Jul 9, 2012 at 3:31 PM, wrote: Paul I issued your command and this is what I got. There is an X in there, but Visit doesn't think that the geometry is in there. (My square duct is 24 x 24 x 36 cells). Rich head -1 sqduct0.f00001 | strings | head -1 #std 4 8 8 8 20736 20736 0.1000000000000E-02 2 0 1 XUP nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/09/2012 04:25 PM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] Using Visit Hi Rich, In principle, this happens automatically. Can you please do the following: head -1 blah | strings | head -1 where "blah" is the name of your first field file ? There should be an "X" in the header indicating that this has the geometry --- if not, I'd like to know about it so that we can fix whatever went wrong. Thanks, Paul On Mon, 9 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Okay, > So how do you ensure that the first field file has the mesh in it as > required by VisIt? > Rich Johnson > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Mon Jul 9 18:02:47 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Mon, 9 Jul 2012 16:02:47 -0700 Subject: [Nek5000-users] Using Visit In-Reply-To: References: Message-ID: Hi Rich, I don't think there should be any problem with a large mesh (we do that regularly). I think there is something different about the file. Can you send me a personal email (hchilds at lbl.gov) so we can iterate through some properties of the file and see if we can narrow down where the problem is? Best, Hank On Mon, Jul 9, 2012 at 3:59 PM, wrote: > > Hank > I am having problems with my large file server. I will have to try again > tomorrow. Do you still want me to send the file? I am wondering if the > problem is that the mesh is too large. It worked okay for a much smaller > mesh. > Rich > > > > > *nek5000-users at lists.mcs.anl.gov* > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > > 07/09/2012 04:47 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > To > nek5000-users at lists.mcs.anl.gov > cc > Subject > Re: [Nek5000-users] Using Visit > > > > > > Hank > The field file is 284 MB. I can try to send it via a large file method > that we have here. > Rich > > > > *nek5000-users at lists.mcs.anl.gov* > Sent by: nek5000-users-bounces at lists.mcs.anl.gov > > 07/09/2012 04:41 PM > Please respond to > nek5000-users at lists.mcs.anl.gov > > To > nek5000-users at lists.mcs.anl.gov > cc > Subject > Re: [Nek5000-users] Using Visit > > > > > > > Hi Rich, > > It sounds like the data is pretty small. Can you send sqduct0.f00001 and > your .nek5000 file to *hchilds at lbl.gov* so I can take a > look? > > Best, > Hank > > On Mon, Jul 9, 2012 at 3:31 PM, <*nek5000-users at lists.mcs.anl.gov*> > wrote: > > Paul > > I issued your command and this is what I got. There is an X in there, but > Visit doesn't think that the geometry is in there. (My square duct is 24 x > 24 x 36 cells). > Rich > > head -1 sqduct0.f00001 | strings | head -1 > #std 4 8 8 8 20736 20736 0.1000000000000E-02 2 > 0 1 XUP > > *nek5000-users at lists.mcs.anl.gov* > Sent by: *nek5000-users-bounces at lists.mcs.anl.gov* > > 07/09/2012 04:25 PM > > > Please respond to* > **nek5000-users at lists.mcs.anl.gov* > > To > *nek5000-users at lists.mcs.anl.gov* > cc > Subject > Re: [Nek5000-users] Using Visit > > > > > > > > > > Hi Rich, > > In principle, this happens automatically. > > Can you please do the following: > > head -1 blah | strings | head -1 > > where "blah" is the name of your first field file ? > > There should be an "X" in the header indicating that this > has the geometry --- if not, I'd like to know about it so > that we can fix whatever went wrong. > > Thanks, > > Paul > > > On Mon, 9 Jul 2012, *nek5000-users at lists.mcs.anl.gov*wrote: > > > Okay, > > So how do you ensure that the first field file has the mesh in it as > > required by VisIt? > > Rich Johnson > > > _______________________________________________ > Nek5000-users mailing list* > **Nek5000-users at lists.mcs.anl.gov* * > **https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users* > > > _______________________________________________ > Nek5000-users mailing list* > **Nek5000-users at lists.mcs.anl.gov* * > **https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users* > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 12 10:34:33 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Jul 2012 09:34:33 -0600 Subject: [Nek5000-users] calling avg_all In-Reply-To: Message-ID: Dear Nek people: I am performing DNS and I want to compute the time mean velocities and pressure as well as the Reynolds stresses. So I tried just doing a simple call to subroutine avg_all from subroutine userchk in the .usr file with no restrictions (no specific time steps, just evey time step). 1st question. Does this accomplish a running time average for the desired variables? 2nd question. I don't want the associated files listing all of the associated variables printed out every time step, only so often. Is this accomplished by setting parameter 68 (iastep) to the frequency of desired outputs? Or does iastep determine how often subroutine avg_all is called as is implied in the .rea file. 3rd question. I tried to look at obtained results in the rms an rms2 files in Visit, but it doesn't recognize the time mean/rms variables. What's up with that? Thanks Rich -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Thu Jul 12 11:35:15 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Jul 2012 11:35:15 -0500 (CDT) Subject: [Nek5000-users] calling avg_all In-Reply-To: References: Message-ID: Hi Rich, avg_all keeps a running tally, normalized by number of steps in the tally, of serveral quantities, and then dumps these and restarts the tallies after each "iastep" (p68) or iostep, if p68=0. So, if p68=500, each tally will be an average entailing 500 timesteps. You can subsequently average these files together to get longer-time averages. The reason you might not want to simply, say, step p68 to 5000 is that sometimes jobs terminate early -- your queue slot ends at lower step than anticipated, etc. So this approach gives the flexibility to subsequently post-process long-time averages. In order to constuct averages from sequences of averages, we need tallies of, for example, u and u^2. This allows one to compute the average, _ _ (1) u =(1/n) sum_i u_i , and the average of the square, ____ _ _ (2) (uu) =(1/n) sum_i u_i u_i , from which we can compute the rms (squared) ____ ____ _ _ (3) (u')^2 = (uu) - u * u In order to able to easily compue the rms from a sequence of files (e.g., as illustrated in (1)--(3)), the rms file contains the u^2 average, the avg file contains the u-average, and these are then combined either with other files, as in (1) and (2), and then together, as in (3), to get the rms. Different users have taken different approaches to (1)--(3). We have some ad hoc averaging tools for the .fld files. For larger runs, most people average by loading multiple f0000 or .fld files into nek5000, from which one can perform all the steps. For many cases, step (3) can also be done in postx. I believe that (3) can also be done in Visit by defining a function of variables -- one tricky thing there is that the u-bar and u^2-bar are coming from different files and I believe that Visit operations are generally applied to operands from the _same_ file (e.g., the same nominal timeslice). Note that the rm2 file contains the cross product running averages, , from which you can get Reynolds stresses, etc. Paul On Thu, 12 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek people: > > I am performing DNS and I want to compute the time mean velocities and > pressure as well as the Reynolds stresses. So I tried just doing a simple > call to subroutine avg_all from subroutine userchk in the .usr file with > no restrictions (no specific time steps, just evey time step). > 1st question. Does this accomplish a running time average for the desired > variables? > 2nd question. I don't want the associated files listing all of the > associated variables printed out every time step, only so often. Is this > accomplished by setting parameter 68 (iastep) to the frequency of desired > outputs? Or does iastep determine how often subroutine avg_all is called > as is implied in the .rea file. > 3rd question. I tried to look at obtained results in the rms an rms2 files > in Visit, but it doesn't recognize the time mean/rms variables. What's up > with that? > > Thanks > Rich > From nek5000-users at lists.mcs.anl.gov Thu Jul 12 12:43:48 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Thu, 12 Jul 2012 11:43:48 -0600 Subject: [Nek5000-users] calling avg_all In-Reply-To: Message-ID: Thanks Paul Rich nek5000-users at lists.mcs.anl.gov Sent by: nek5000-users-bounces at lists.mcs.anl.gov 07/12/2012 10:35 AM Please respond to nek5000-users at lists.mcs.anl.gov To nek5000-users at lists.mcs.anl.gov cc Subject Re: [Nek5000-users] calling avg_all Hi Rich, avg_all keeps a running tally, normalized by number of steps in the tally, of serveral quantities, and then dumps these and restarts the tallies after each "iastep" (p68) or iostep, if p68=0. So, if p68=500, each tally will be an average entailing 500 timesteps. You can subsequently average these files together to get longer-time averages. The reason you might not want to simply, say, step p68 to 5000 is that sometimes jobs terminate early -- your queue slot ends at lower step than anticipated, etc. So this approach gives the flexibility to subsequently post-process long-time averages. In order to constuct averages from sequences of averages, we need tallies of, for example, u and u^2. This allows one to compute the average, _ _ (1) u =(1/n) sum_i u_i , and the average of the square, ____ _ _ (2) (uu) =(1/n) sum_i u_i u_i , from which we can compute the rms (squared) ____ ____ _ _ (3) (u')^2 = (uu) - u * u In order to able to easily compue the rms from a sequence of files (e.g., as illustrated in (1)--(3)), the rms file contains the u^2 average, the avg file contains the u-average, and these are then combined either with other files, as in (1) and (2), and then together, as in (3), to get the rms. Different users have taken different approaches to (1)--(3). We have some ad hoc averaging tools for the .fld files. For larger runs, most people average by loading multiple f0000 or .fld files into nek5000, from which one can perform all the steps. For many cases, step (3) can also be done in postx. I believe that (3) can also be done in Visit by defining a function of variables -- one tricky thing there is that the u-bar and u^2-bar are coming from different files and I believe that Visit operations are generally applied to operands from the _same_ file (e.g., the same nominal timeslice). Note that the rm2 file contains the cross product running averages, , from which you can get Reynolds stresses, etc. Paul On Thu, 12 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Dear Nek people: > > I am performing DNS and I want to compute the time mean velocities and > pressure as well as the Reynolds stresses. So I tried just doing a simple > call to subroutine avg_all from subroutine userchk in the .usr file with > no restrictions (no specific time steps, just evey time step). > 1st question. Does this accomplish a running time average for the desired > variables? > 2nd question. I don't want the associated files listing all of the > associated variables printed out every time step, only so often. Is this > accomplished by setting parameter 68 (iastep) to the frequency of desired > outputs? Or does iastep determine how often subroutine avg_all is called > as is implied in the .rea file. > 3rd question. I tried to look at obtained results in the rms an rms2 files > in Visit, but it doesn't recognize the time mean/rms variables. What's up > with that? > > Thanks > Rich > _______________________________________________ Nek5000-users mailing list Nek5000-users at lists.mcs.anl.gov https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sun Jul 15 11:09:54 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 15 Jul 2012 12:09:54 -0400 Subject: [Nek5000-users] Passive Scalar Initialization Message-ID: Hi, I want to start solving the passive scalar equation after the background flow field has reached certain characteristics. Is it possible to defer the solution of the passive scalar and then initialize it at sometime t>0? In this case, should I include the passive scalar boundary condition data in the rea and usr files from the beginning? Thanks for your help. Regards, Alireza From nek5000-users at lists.mcs.anl.gov Sun Jul 15 11:44:30 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 15 Jul 2012 11:44:30 -0500 (CDT) Subject: [Nek5000-users] Passive Scalar Initialization In-Reply-To: References: Message-ID: Hi Alireza, You can alway reinitialize any field, so either start with or without, whichever is easiest. If it's a long and expensive run (esp. from a passive scalar standpoint, for example if you have very low Pr), then you might choose to not carry the PS along till you get to your desired background flow state. Otherwise, PS typically costs much less than the hydro, so carrying PS along is not an excessive burden and the setup and logistics overhead is sometimes easier just to deal with it at the outset. I hope this helps. Cheers, Paul On Sun, 15 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > I want to start solving the passive scalar equation after the background flow > field has reached certain characteristics. Is it possible to defer the > solution of the passive scalar and then initialize it at sometime t>0? In > this case, should I include the passive scalar boundary condition data in the > rea and usr files from the beginning? > > Thanks for your help. > > Regards, > Alireza > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Jul 15 12:09:00 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 15 Jul 2012 13:09:00 -0400 Subject: [Nek5000-users] Passive Scalar Initialization In-Reply-To: References: Message-ID: Hi, Thanks for your hint. So, how can I reinitialize the PS after some time? Should I call useric at userchk? And as I have two passive scalars, how can I make sure that just one of them is initialized and the other one and the flow field are read from the restarting fld file? Thanks again. Regards, Alireza Quoting nek5000-users at lists.mcs.anl.gov: > > Hi Alireza, > > You can alway reinitialize any field, so either start with or without, > whichever is easiest. If it's a long and expensive run (esp. from > a passive scalar standpoint, for example if you have very low Pr), then > you might choose to not carry the PS along till you get to your desired > background flow state. Otherwise, PS typically costs much less than the > hydro, so carrying PS along is not an excessive burden and the setup > and logistics overhead is sometimes easier just to deal with it at > the outset. > > I hope this helps. > > Cheers, > > Paul > > > On Sun, 15 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi, >> >> I want to start solving the passive scalar equation after the >> background flow field has reached certain characteristics. Is it >> possible to defer the solution of the passive scalar and then >> initialize it at sometime t>0? In this case, should I include the >> passive scalar boundary condition data in the rea and usr files >> from the beginning? >> >> Thanks for your help. >> >> Regards, >> Alireza >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Sun Jul 15 12:28:09 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 15 Jul 2012 12:28:09 -0500 (CDT) Subject: [Nek5000-users] Passive Scalar Initialization In-Reply-To: References: Message-ID: Hi Alireza, userchk() is the correct place to intervene. It is called after the end of each timestep, including "Step 0", which constitutes the initialization. Hence, on step 0, you have the chance to reset any variable prior to the start of Step 1, without worry of it being overwritten by some other initialization phase. So, I would do the following in userchk, for the particular instance of when you want to do your initialization. n=nx1*ny1*nz1*nelt if (istep.eq.0) then do i=1,n x=xm1(i,1,1,1) y=ym1(i,1,1,1) z=zm1(i,1,1,1) t(i,1,1,1,1) = x*x + y-z (or whatever...) enddo endif If you instead would wish to read a result in from a .fld file, this can also be done. You simply modify your .rea file to read 2 files instead of one. The first can have the velocity and the second the passive scalar, say. Cheers, Paul On Sun, 15 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Hi, > > Thanks for your hint. So, how can I reinitialize the PS after some time? > Should I call useric at userchk? And as I have two passive scalars, how can I > make sure that just one of them is initialized and the other one and the flow > field are read from the restarting fld file? > > Thanks again. > > Regards, > Alireza > > > > > > Quoting nek5000-users at lists.mcs.anl.gov: > >> >> Hi Alireza, >> >> You can alway reinitialize any field, so either start with or without, >> whichever is easiest. If it's a long and expensive run (esp. from >> a passive scalar standpoint, for example if you have very low Pr), then >> you might choose to not carry the PS along till you get to your desired >> background flow state. Otherwise, PS typically costs much less than the >> hydro, so carrying PS along is not an excessive burden and the setup >> and logistics overhead is sometimes easier just to deal with it at >> the outset. >> >> I hope this helps. >> >> Cheers, >> >> Paul >> >> >> On Sun, 15 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: >> >>> Hi, >>> >>> I want to start solving the passive scalar equation after the background >>> flow field has reached certain characteristics. Is it possible to defer >>> the solution of the passive scalar and then initialize it at sometime t>0? >>> In this case, should I include the passive scalar boundary condition data >>> in the rea and usr files from the beginning? >>> >>> Thanks for your help. >>> >>> Regards, >>> Alireza >>> >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >> > > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sun Jul 15 16:21:27 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sun, 15 Jul 2012 17:21:27 -0400 Subject: [Nek5000-users] Passive Scalar Initialization In-Reply-To: References: Message-ID: Hi, I'm deeply grateful for your help. I have another question regarding I/O procedure. At each time and on every grid point, I calculate some angles (scalar quantities) which are functions of the vorticity and their own values from the previous time step. I need to store the values of these angles at the last time step (preferably in a separate file) and then recall those values after restating the simulation. I think I should use outpost2 to store the values, but I'm not sure how to open a different file other than fld file and then how to read that file to be consistent in parallel. I wonder if you have any hint. Regards, Alireza Quoting nek5000-users at lists.mcs.anl.gov: > > Hi Alireza, > > userchk() is the correct place to intervene. > > It is called after the end of each timestep, including "Step 0", > which constitutes the initialization. > > Hence, on step 0, you have the chance to reset any variable prior > to the start of Step 1, without worry of it being overwritten by > some other initialization phase. > > So, I would do the following in userchk, for the particular > instance of when you want to do your initialization. > > > n=nx1*ny1*nz1*nelt > > if (istep.eq.0) then > do i=1,n > x=xm1(i,1,1,1) > y=ym1(i,1,1,1) > z=zm1(i,1,1,1) > t(i,1,1,1,1) = x*x + y-z (or whatever...) > enddo > endif > > If you instead would wish to read a result in from a .fld file, > this can also be done. You simply modify your .rea file to > read 2 files instead of one. The first can have the velocity > and the second the passive scalar, say. > > Cheers, > > Paul > > > On Sun, 15 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi, >> >> Thanks for your hint. So, how can I reinitialize the PS after some >> time? Should I call useric at userchk? And as I have two passive >> scalars, how can I make sure that just one of them is initialized >> and the other one and the flow field are read from the restarting >> fld file? >> >> Thanks again. >> >> Regards, >> Alireza >> >> >> >> >> >> Quoting nek5000-users at lists.mcs.anl.gov: >> >>> >>> Hi Alireza, >>> >>> You can alway reinitialize any field, so either start with or without, >>> whichever is easiest. If it's a long and expensive run (esp. from >>> a passive scalar standpoint, for example if you have very low Pr), then >>> you might choose to not carry the PS along till you get to your desired >>> background flow state. Otherwise, PS typically costs much less than the >>> hydro, so carrying PS along is not an excessive burden and the setup >>> and logistics overhead is sometimes easier just to deal with it at >>> the outset. >>> >>> I hope this helps. >>> >>> Cheers, >>> >>> Paul >>> >>> >>> On Sun, 15 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: >>> >>>> Hi, >>>> >>>> I want to start solving the passive scalar equation after the >>>> background flow field has reached certain characteristics. Is it >>>> possible to defer the solution of the passive scalar and then >>>> initialize it at sometime t>0? In this case, should I include the >>>> passive scalar boundary condition data in the rea and usr files >>>> from the beginning? >>>> >>>> Thanks for your help. >>>> >>>> Regards, >>>> Alireza >>>> >>>> _______________________________________________ >>>> Nek5000-users mailing list >>>> Nek5000-users at lists.mcs.anl.gov >>>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> _______________________________________________ >>> Nek5000-users mailing list >>> Nek5000-users at lists.mcs.anl.gov >>> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >>> >> >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > From nek5000-users at lists.mcs.anl.gov Wed Jul 18 14:12:13 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Jul 2012 12:12:13 -0700 (PDT) Subject: [Nek5000-users] Post-Processing Message-ID: Hi,? I'm am very new at this so please forgive me for stupid questions, simple mistakes, and lack or technical lingo. I'm running two flow case simulations, a turbulent channel and a backward facing step to test a new LES filter. I have run the simulation including the avg_all routine. After completion, several avg.f, rms.f, and rm2.f files were created. I compiled the avgall.usr file and ran again after placing the .f files into respective .list files and ran again in order to get the time averaged data. In the .output file, a bunch of error messages were displayed saying ERROR: Non-positive diffusivity (0.00) specified for field 1, group 0 element. I was told that commenting out the udiff and utrans in the uservp subroutine of the avgall.usr file and also setting the NSTEPS to 0 in the .rea file would fix the problem, but neither worked. Any advice? ? Sincerely, Josh Rabau Mechanical Engineering MS Texas A&M University 2013 Mechanical Engineering BS Rochester Institute of Technology 2011 603-381-6685 josh.rabau at yahoo.com jir2830 at .tamu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Wed Jul 18 14:57:29 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Wed, 18 Jul 2012 12:57:29 -0700 (PDT) Subject: [Nek5000-users] Post-Processing Message-ID: I figured it out. the solution was instead of commenting out the udiff and utrans lines in the .usr file, setting them to 1 instead ? Sincerely, Josh Rabau Mechanical Engineering MS Texas A&M University 2013 Mechanical Engineering BS Rochester Institute of Technology 2011 603-381-6685 josh.rabau at yahoo.com jir2830 at .tamu.edu -------------- next part -------------- An HTML attachment was scrubbed... URL: From nek5000-users at lists.mcs.anl.gov Sat Jul 21 10:24:08 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 21 Jul 2012 11:24:08 -0400 Subject: [Nek5000-users] Restart Problem Message-ID: Hi Neks, I have a question regarding I/O procedure. At each time and on every grid point, I integrate the components of a vector field in time which are functions of the vorticity and their own values from the previous time step. I need to store the values of these components at the last time step (preferably in a separate file) and then recall those values after restarting the simulation. I think I should use outpost2 to store the values, but I'm not sure how to open a different file other than fld file and then how to read that file to be consistent in parallel. I wonder if you have any hint. Regards, Alireza From nek5000-users at lists.mcs.anl.gov Sat Jul 21 11:08:44 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 21 Jul 2012 11:08:44 -0500 (CDT) Subject: [Nek5000-users] Restart Problem In-Reply-To: References: Message-ID: Hi Alireza, I would suggest looking closely at the subroutine "my_full_restart" in the cyl_restart example .usr files. I think from there you can figure out how to accomplish your goal. Please let me know if that gets you to where you need to be. If I were you, I would use outpost(), rather than outpost2(). Both outpost (or outpost2) and my_full_restart are fully parallel so nothing special required in that respect. Paul On Sat, 21 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > Hi Neks, > > I have a question regarding I/O procedure. At each time and on every grid > point, I integrate the components of a vector field in time which are > functions of the vorticity and their own values from the previous time step. > I need to store the values of these components at the last time step > (preferably in a separate file) and then recall those values after restarting > the simulation. I think I should use outpost2 to store the values, but I'm > not sure how to open a different file other than fld file and then how to > read that file to be consistent in parallel. I wonder if you have any hint. > > > Regards, > Alireza > > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users From nek5000-users at lists.mcs.anl.gov Sat Jul 21 11:30:03 2012 From: nek5000-users at lists.mcs.anl.gov (nek5000-users at lists.mcs.anl.gov) Date: Sat, 21 Jul 2012 11:30:03 -0500 (CDT) Subject: [Nek5000-users] Restart Problem In-Reply-To: References: Message-ID: Sorry --- Looking again at my_full_restart, I see that it and the routines it calls are both very streamlined and don't expose the variables of interest. Typically, I would do something of the following form, borrowing from "full_restart" in ic.f: call opcopy(vxt,vyt,vzt,vx,vy,vz) ! Save vx,vy,vz call chcopy (initc,s80(ifile),80) ! Load your field of interest call bcast (initc,80) call restart (1) call opcopy(u1,u2,u3,vx,vy,vz) ! Save your field in u1-u3 call opcopy(vx,vy,vz,vxt,vyt,vzt) ! Restore vx,vy,vz Be sure you declare vxt,vyt,vzt, u1,u2,u3, etc. to be fields of size lx1*ly1*lz1*lelt, each. I would encapsulate the above in a routine that is called from userchk() as needed when istep=0 (for initial conditions) and for istep=1,2 if you wish to boot up (e.g., as done in full-restart). Paul On Sat, 21 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > > Hi Alireza, > > I would suggest looking closely at the subroutine "my_full_restart" > in the cyl_restart example .usr files. I think from there you can > figure out how to accomplish your goal. > > Please let me know if that gets you to where you need to be. > > If I were you, I would use outpost(), rather than outpost2(). > > Both outpost (or outpost2) and my_full_restart are fully parallel > so nothing special required in that respect. > > Paul > > > > On Sat, 21 Jul 2012, nek5000-users at lists.mcs.anl.gov wrote: > >> Hi Neks, >> >> I have a question regarding I/O procedure. At each time and on every grid >> point, I integrate the components of a vector field in time which are >> functions of the vorticity and their own values from the previous time >> step. I need to store the values of these components at the last time step >> (preferably in a separate file) and then recall those values after >> restarting the simulation. I think I should use outpost2 to store the >> values, but I'm not sure how to open a different file other than fld file >> and then how to read that file to be consistent in parallel. I wonder if >> you have any hint. >> >> >> Regards, >> Alireza >> >> _______________________________________________ >> Nek5000-users mailing list >> Nek5000-users at lists.mcs.anl.gov >> https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users > _______________________________________________ > Nek5000-users mailing list > Nek5000-users at lists.mcs.anl.gov > https://lists.mcs.anl.gov/mailman/listinfo/nek5000-users >