Re: [gridengine users] Sorting qhost and choosing qstat columns
I would definitely not recommend parsing XML in bash (or any other language that doesn't implement nested data structures), but Perl XML::LibXML has been a handy library for implementing our custom parsing of q* XML output. These days I would probably use Python or Ruby but I wrote our tools many years ago so Perl it was... On Thu, Aug 01, 2019 at 10:59:09AM -0400, David Trimboli wrote: > Changing the names isn't an option; I inherited these names years ago and > nobody's going to want me to change them because I want to see something in > order. :) > > Basically, I can run this command to see it the way I want it: > qhost | head -n 3; qhost | tail -n +4 | sort -V > but of course this is cumbersome and makes adding options a chore. (Suppose > I want to use -j?) > > I guess XML it is. If this were PowerShell it'd be a cinch, but working in > Bash... ugh... > > On 8/1/2019 10:39 AM, MacMullan IV, Hugh wrote: > > David, > > > > Best for qhost sort would be to change your 'cluster' names to zero-padded, > > if you really want that kind of sorting. Or you could create an alias like > > 'qhost | sort -nk 1.8', assuming 'clusterX' is always true (the 8th > > character is where you start the sort). > > > > As Skylar says, if you want a custom qstat, you should probably build one > > from the '-xml' output. > > > > Regards, > > -Hugh > > > > -Original Message- > > From: users-boun...@gridengine.org On Behalf > > Of David Trimboli > > Sent: Thursday, August 1, 2019 9:59 AM > > To: users Users > > Subject: [gridengine users] Sorting qhost and choosing qstat columns > > > > When I run qhost, the output is sorted alphabetically ??? which means > > "cluster10" appears before "cluster2," and so on. > > > > Before I go writing bash functions to manually sort this, which might > > lead to output side-effects, is there any way to change the sort to a > > natural number sort, so that "cluster2" would appear before "cluster10," > > etc.? > > > > When I run qstat, the normal wraps to a second line in my terminal set > > to 120 columns. I could fix that by eliminating the "jclass" column, > > which doesn't contain any information, but I can only find ways to add > > columns, not take them away. Is there a way to make this column go away? > > > > ___ > > users mailing list > > users@gridengine.org > > https://urldefense.proofpoint.com/v2/url?u=https-3A__gridengine.org_mailman_listinfo_users=DwIGaQ=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y=EKk3zFVROsf8w5OyB2T6u55jzploih3y7CaWIlGOLAY=m_wX_jPeroRg7CYImv_hhYP5_j4Yg77eKMrgzOYGdVY=pwdLspfOZXCXUKlxE7OGCCu9y5Pg8hqoWxsY3gcb6Ls= > ___ > users mailing list > users@gridengine.org > https://gridengine.org/mailman/listinfo/users -- -- Skylar Thompson (skyl...@u.washington.edu) -- Genome Sciences Department, System Administrator -- Foege Building S046, (206)-685-7354 -- University of Washington School of Medicine ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] Sorting qhost and choosing qstat columns
On 8/1/2019 11:24 AM, Reuti wrote: Hi, Am 01.08.2019 um 15:58 schrieb David Trimboli : When I run qhost, the output is sorted alphabetically — which means "cluster10" appears before "cluster2," and so on. Before I go writing bash functions to manually sort this, which might lead to output side-effects, is there any way to change the sort to a natural number sort, so that "cluster2" would appear before "cluster10," etc.? When I run qstat, the normal wraps to a second line in my terminal set to 120 columns. I could fix that by eliminating the "jclass" column, which doesn't contain any information, but I can only find ways to add columns, not take them away. Is there a way to make this column go away? Besides `cut -b`: what type of output are you looking for? There is a `qstatus` AWK script in SoGE which displays the relevant columns including a longer job name. -- Reuti Hmm, good point! This seems to do what I need: qstat -u '*' | cut -b 1-100,121-140 ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] Sorting qhost and choosing qstat columns
Hi On 01/08/2019 15:59, David Trimboli wrote: I guess XML it is. If this were PowerShell it'd be a cinch, but working in Bash... ugh... I'm not a PowerShell user, but I believe it is available for Linux. This should help, unless you are prevented from installing it on your cluster due to local policies! Cheers, Fred ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] Sorting qhost and choosing qstat columns
Hi, > Am 01.08.2019 um 15:58 schrieb David Trimboli : > > When I run qhost, the output is sorted alphabetically — which means > "cluster10" appears before "cluster2," and so on. > > Before I go writing bash functions to manually sort this, which might lead to > output side-effects, is there any way to change the sort to a natural number > sort, so that "cluster2" would appear before "cluster10," etc.? > When I run qstat, the normal wraps to a second line in my terminal set to 120 > columns. I could fix that by eliminating the "jclass" column, which doesn't > contain any information, but I can only find ways to add columns, not take > them away. Is there a way to make this column go away? Besides `cut -b`: what type of output are you looking for? There is a `qstatus` AWK script in SoGE which displays the relevant columns including a longer job name. -- Reuti ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] Sorting qhost and choosing qstat columns
Changing the names isn't an option; I inherited these names years ago and nobody's going to want me to change them because I want to see something in order. :) Basically, I can run this command to see it the way I want it: qhost | head -n 3; qhost | tail -n +4 | sort -V but of course this is cumbersome and makes adding options a chore. (Suppose I want to use -j?) I guess XML it is. If this were PowerShell it'd be a cinch, but working in Bash... ugh... On 8/1/2019 10:39 AM, MacMullan IV, Hugh wrote: David, Best for qhost sort would be to change your 'cluster' names to zero-padded, if you really want that kind of sorting. Or you could create an alias like 'qhost | sort -nk 1.8', assuming 'clusterX' is always true (the 8th character is where you start the sort). As Skylar says, if you want a custom qstat, you should probably build one from the '-xml' output. Regards, -Hugh -Original Message- From: users-boun...@gridengine.org On Behalf Of David Trimboli Sent: Thursday, August 1, 2019 9:59 AM To: users Users Subject: [gridengine users] Sorting qhost and choosing qstat columns When I run qhost, the output is sorted alphabetically — which means "cluster10" appears before "cluster2," and so on. Before I go writing bash functions to manually sort this, which might lead to output side-effects, is there any way to change the sort to a natural number sort, so that "cluster2" would appear before "cluster10," etc.? When I run qstat, the normal wraps to a second line in my terminal set to 120 columns. I could fix that by eliminating the "jclass" column, which doesn't contain any information, but I can only find ways to add columns, not take them away. Is there a way to make this column go away? ___ users mailing list users@gridengine.org https://urldefense.proofpoint.com/v2/url?u=https-3A__gridengine.org_mailman_listinfo_users=DwIGaQ=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y=EKk3zFVROsf8w5OyB2T6u55jzploih3y7CaWIlGOLAY=m_wX_jPeroRg7CYImv_hhYP5_j4Yg77eKMrgzOYGdVY=pwdLspfOZXCXUKlxE7OGCCu9y5Pg8hqoWxsY3gcb6Ls= ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] Sorting qhost and choosing qstat columns
David, Best for qhost sort would be to change your 'cluster' names to zero-padded, if you really want that kind of sorting. Or you could create an alias like 'qhost | sort -nk 1.8', assuming 'clusterX' is always true (the 8th character is where you start the sort). As Skylar says, if you want a custom qstat, you should probably build one from the '-xml' output. Regards, -Hugh -Original Message- From: users-boun...@gridengine.org On Behalf Of David Trimboli Sent: Thursday, August 1, 2019 9:59 AM To: users Users Subject: [gridengine users] Sorting qhost and choosing qstat columns When I run qhost, the output is sorted alphabetically — which means "cluster10" appears before "cluster2," and so on. Before I go writing bash functions to manually sort this, which might lead to output side-effects, is there any way to change the sort to a natural number sort, so that "cluster2" would appear before "cluster10," etc.? When I run qstat, the normal wraps to a second line in my terminal set to 120 columns. I could fix that by eliminating the "jclass" column, which doesn't contain any information, but I can only find ways to add columns, not take them away. Is there a way to make this column go away? ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users ___ users mailing list users@gridengine.org https://gridengine.org/mailman/listinfo/users
Re: [gridengine users] Sorting qhost and choosing qstat columns
I'm not aware of any way to change the sort order or remove columns without
other side-effects (though I do note that "qstat -f" does not have the
column), but both of these commands do have a XML output option ("-xml")
which you could use to write your own reporting utilities.
On Thu, Aug 01, 2019 at 09:58:49AM -0400, David Trimboli wrote:
> When I run qhost, the output is sorted alphabetically ??? which means
> "cluster10" appears before "cluster2," and so on.
>
> Before I go writing bash functions to manually sort this, which might lead
> to output side-effects, is there any way to change the sort to a natural
> number sort, so that "cluster2" would appear before "cluster10," etc.?
>
> When I run qstat, the normal wraps to a second line in my terminal set to
> 120 columns. I could fix that by eliminating the "jclass" column, which
> doesn't contain any information, but I can only find ways to add columns,
> not take them away. Is there a way to make this column go away?
>
> ___
> users mailing list
> users@gridengine.org
> https://gridengine.org/mailman/listinfo/users
--
-- Skylar Thompson (skyl...@u.washington.edu)
-- Genome Sciences Department, System Administrator
-- Foege Building S046, (206)-685-7354
-- University of Washington School of Medicine
___
users mailing list
users@gridengine.org
https://gridengine.org/mailman/listinfo/users
