# Updating Suite u-cp976

**URL:** <https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735>\
**Category:** JULES\
**Tags:** Monsoon2\
**Created:** [29 September 2022 13:55 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735 "2022-09-29T13:55:08Z")\
**Posts on this page:** 18\
**Page:** 2

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [17 October 2022 12:02 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/21 "2022-10-17T12:02:36Z")

</div>

Hi Ayesha  
Excellent! Thank you!  
Patrick

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<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [24 October 2022 11:56 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/22 "2022-10-24T11:56:39Z")

</div>

Hi Patrick,

I’ve tried running u-cp976 with the prebuild jules.exe and I get this error with the spinup fails:

…  
[WARN] file:jules\_deposition.nml: skip missing optional source: namelist:jules\_deposition\_species(🙂  
[WARN] file:ancillaries.nml: skip missing optional source: namelist:jules\_flake  
[WARN] file:ancillaries.nml: skip missing optional source: namelist:urban\_properties  
[WARN] file:imogen.nml: skip missing optional source: namelist:imogen\_run\_list  
[WARN] file:cable\_surface\_types.nml: skip missing optional source: namelist:cable\_surface\_types  
[FAIL] $RUN\_JULES # return-code=139  
2022-10-24T11:52:20Z CRITICAL - failed/EXIT

does the RUN\_JULES error mean that there is a problem with jules.exe or is it something else?

Thanks,

Ayesha

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [24 October 2022 12:50 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/23 "2022-10-24T12:50:06Z")

</div>

Hi Ayesha  
I am not sure where the problem is, whether it is with the JULES pre-built executable, or with something else. Have you tried to run the jules.exe pre-build from the command line? If that pre-build runs ok, or at least gives less cryptic errors, then it could be a problem with your suite.

Are you trying to run the pre-build on an INTEL node of JASMIN or and AMD node? Did you compile it on the same type of node?  
Patrick

---

<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [24 October 2022 13:07 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/24 "2022-10-24T13:07:12Z")

</div>

Hi Patrick,  
How do I run jules.exe from the command line?  
I’m on Monsoon, so I’m not sure what node I’m on sorry. Do you know how I find out? I used this to make jules.exe:  
export JULES\_PLATFORM=meto-xc40-cce  
export JULES\_BUILD=fast  
export JULES\_NETCDF=netcdf

Thanks,  
Ayesha

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [24 October 2022 16:56 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/25 "2022-10-24T16:56:04Z")

</div>

Hi Ayesha  
To run the jules executable from the command line, first locate the jules.exe pre-build that you compiled. Then change to that directory, and type:  
`./jules.exe`

That should give some error message since it isn’t pointing to the JULES namelists, but at least it will show that it is properly compiled. If that doesn’t work, it’s possible that on Monsoon, you need to load some modules before running jules.exe from the command line.

If it does try to start running properly, then maybe you can also look at your job.out and job.err log files to look for more detailed error messages from when you try to run jules with Rose/Cylc?

I had forgotten that you are working on Monsoon. So disregard my comments about running on the same processor-type as you compile on. Those comments were for the JASMIN platform.  
Patrick

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<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [25 October 2022 08:54 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/26 "2022-10-25T08:54:14Z")

</div>

Hi Patrick,

Yeah it looks like jules.exe is the issue. I tried loading the modules that I loaded before to build it but it still didn’t work:

ahussain@xcslc0:~/MODELS/vn6.1\_jules/build/bin\> ls  
jules.exe rose-jules-run  
ahussain@xcslc0:~/MODELS/vn6.1\_jules/build/bin\> ./jules.exe  
[Tue Oct 25 08:51:13 2022] [unknown] Fatal error in MPI\_Init: Other MPI error, error stack:  
MPIR\_Init\_thread(506):  
MPID\_Init(192)…: channel initialization failed  
MPID\_Init(569)…: PMI2 init failed: 1  
ahussain@xcslc0:~/MODELS/vn6.1\_jules/build/bin\> module swap PrgEnv-cray PrgEnv-cray/5.2.82  
ahussain@xcslc0:~/MODELS/vn6.1\_jules/build/bin\> module load cray-netcdf-hdf5parallel/4.3.2  
ahussain@xcslc0:~/MODELS/vn6.1\_jules/build/bin\> module load cray-snplauncher/7.0.4  
ahussain@xcslc0:~/MODELS/vn6.1\_jules/build/bin\> ./jules.exe  
[Tue Oct 25 08:52:19 2022] [unknown] Fatal error in MPI\_Init: Other MPI error, error stack:  
MPIR\_Init\_thread(506):  
MPID\_Init(192)…: channel initialization failed  
MPID\_Init(569)…: PMI2 init failed: 1

Do you know which modules I should load to get jules.exe to work?

Thanks,

Ayesha

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [25 October 2022 09:53 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/27 "2022-10-25T09:53:54Z")

</div>

Hi Ayesha:  
Since your prebuild is MPI capable, to test to see if your prebuild is working or not, you might have to do something like `mpirun jules.exe`, to test if it is at all close to being compiled properly. There might be more settings to try, in order to get the mpirun to work properly.

It could be much easier for both of us and for others in the future (if you already have u-al752 working on Monsoon), to take the build capability of u-al752 and put that build capability in your new suites. This is the 3rd time I suggested this.  
Patrick

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<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [25 October 2022 10:02 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/28 "2022-10-25T10:02:06Z")

</div>

Hi Patrick,

Sorry about all of this, I really appreciate you helping me! The main reason why I want to do this myself is that eventually, I’ll have development versions of JULES to run through the suite, which I’ll have compiled elsewhere on my system while making the code changes.

I’ll try the u-al752 method now.

Thanks,

Ayesha

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<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [25 October 2022 18:06 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/29 "2022-10-25T18:06:59Z")

</div>

Hi Ayesha:  
No need to be sorry. I am glad to try to help. And I am glad that you’re now trying to integrate the build process in the suite.

You can use the suite to do the builds of the development versions of JULES, instead of building it elsewhere. You can also have a Boolean flags called BUILD and RUN that you can set up in your rose-suite.conf file, so that the suite knows if you want to build/make the JULES executable or not and if you want to run JULES or not.

Then, you can run the suite during code development with BUILD=true and RUN=false. Next, when you want to run JULES after a successful build, you can save a bit of time by running the suite with BUILD=false and RUN=true. Then later, if you or anyone else wants to run the suite in full, they can just set BUILD=true and RUN=true.

The suite u-al752 doesn’t have such Boolean flags for BUILD and RUN, but the unrelated suite u-bb316 does have the Boolean flag for BUILD, if you’d like to look at how BUILD is used in the suite.rc file for that suite.  
Patrick

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<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [25 October 2022 19:03 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/30 "2022-10-25T19:03:40Z")

</div>

Hi Ayesha:  
Also, to test out new JULES FORTRAN code with a suite like u-al752, all one really needs to do is point the suite to the new FORTRAN code, by changing the `rose-suite.conf` file from:

```auto
JULES_FCM='fcm:jules.x_tr'
JULES_REVISION='21512'
RUNID='JULES_vn6.2'

```

to something like:

```auto
#this would point to your new branch that you have checked in to MOSRS:
JULES_FCM='fcm:jules.x_br/dev/patrickmcguire/vn6.2_branch'
#this would be the appropriate revision number for this hypothetical branch:
JULES_REVISION='24113' 
RUNID='JULES_vn6.2_branch'

```

If you want to just practice building the JULES code with the u-al752 suite, you can start the suite running, and then put a hold on the JULES app, so that it doesn’t run after the fcm\_make task builds JULES.

Patrick

---

<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [26 October 2022 14:59 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/31 "2022-10-26T14:59:45Z")

</div>

Hi Patrick,

Thank you, that makes sense! I copied over the fcm\_make folder from u-al752 (so the rose-app.conf and fcm-make.cfg),

I also changed rose-suite.conf so it is now:  
MAKE\_PLOTS=True  
SKIP\_SPINUP=True  
L\_TOP=True  
L\_IRRIG\_DMD=False  
L\_TRIFFID\_N=True  
LOCATION=‘MONSOON’  
#JULES\_EXE=‘/home/d03/ahussain/MODELS/vn6.2\_jules/build/bin/jules.exe’  
BUILD=True  
JULES\_FCM=‘fcm:jules.xm\_tr’  
JULES\_REVISION=‘21512’

I saw that there’s information on fcm\_make in site/suite.rc.MONSOON, which I point to in the rose-suite.conf file. I’m not sure whether I’m already using this or not though?

I added this to suite.rc in the [runtime] area:

[[fcm\_make]]  
inherit = None, FCM\_MAKE\_{{ LOCATION }}

And I changed the [scheduling] section to this:

```
[[dependencies]]
    graph = """
{%- if BUILD %}
    JULES_REVISION = {{ JULES_REVISION }}
    JULES_FCM = {{ JULES_FCM }}
    {%- if JULES_REVISION == '' %}
        AT_JULES_REVISION = ''
    {%- else %}
        AT_JULES_REVISION= @{{ JULES_REVISION }}
    {%- endif %}
    {%- if not SKIP_SPINUP %}
        fcm_make => SPINUP_RUNS
        SPINUP_RUNS:finish-all & SPINUP_RUNS:succeed-all => MAIN_RUNS
    {%- else %}
        fcm_make => MAIN_RUNS
    {%- endif %}
{%- else %}
    {%- if not SKIP_SPINUP %}
        SPINUP_RUNS
        SPINUP_RUNS:finish-all & SPINUP_RUNS:succeed-all => MAIN_RUNS
    {%- else %}
        MAIN_RUNS
    {%- endif %}
{%- endif %}
{%- if MAKE_PLOTS %}
    MAIN_RUNS:finish-all & MAIN_RUNS:succeed-all => make_plots
{%- endif %}
    """

```

and changed the [[jules]] part to this:  
[[jules]]  
inherit = None, JULES\_{{ LOCATION }}  
{%- if BUILD %}  
script = “rose task-run --path= --path=share/fcm\_make/build/bin”  
{%- else %}  
script = “rose task-run --path= --path=`dirname {{JULES_EXE}}`”  
{%- endif %}

I kept everything else the same (sorry if this is confusing to read, I wasn’t sure how best to show you this).

I then tried running the suite and I got this:  
ahussain@xcslc0:~/roses/u-cp976\> rose suite-run --new  
[INFO] export CYLC\_VERSION=7.8.12  
[INFO] export ROSE\_ORIG\_HOST=xcslc0  
[INFO] export ROSE\_SITE=  
[INFO] export ROSE\_VERSION=2019.01.7  
[INFO] delete: localhost:cylc-run/u-cp976  
[INFO] symlink: /projects/intimp/ahussain/cylc-run/u-cp976 \<= /home/d03/ahussain/cylc-run/u-cp976  
[INFO] create: log.20221026T145820Z  
[INFO] delete: log  
[INFO] symlink: log.20221026T145820Z \<= log  
[INFO] log.20221026T144451Z.tar.gz \<= log.20221026T144451Z  
[INFO] delete: log.20221026T144451Z/  
[INFO] create: log/suite  
[INFO] create: log/rose-conf  
[INFO] symlink: rose-conf/20221026T145820-run.conf \<= log/rose-suite-run.conf  
[INFO] symlink: rose-conf/20221026T145820-run.version \<= log/rose-suite-run.version  
[INFO] install: site/suite.rc.MONSOON  
[INFO] source: [https://code.metoffice.gov.uk/svn/roses-u/a/l/7/5/2/trunk/site/suite.rc.MONSOON@207939](https://code.metoffice.gov.uk/svn/roses-u/a/l/7/5/2/trunk/site/suite.rc.MONSOON@207939)  
[INFO] REGISTERED u-cp976 → /home/d03/ahussain/cylc-run/u-cp976  
**[FAIL]** cylc validate -o /working/d03/ahussain/jtmp/tmp.qDsXNSyrhA/tmpXpcWD7 --strict u-cp976 # return-code=1, stderr=  
**[FAIL]** WARNING - deprecated items were automatically upgraded in ‘suite definition’:  
**[FAIL]** WARNING - \* (6.4.0) [runtime][make\_plots][command scripting] → [runtime][make\_plots][script] - value unchanged  
**[FAIL]** WARNING - naked dummy tasks detected (no entry under [runtime]):  
**[FAIL]** + 21512  
**[FAIL]** + AT\_JULES\_REVISION  
**[FAIL]** + JULES\_FCM  
**[FAIL]** + JULES\_REVISION  
**[FAIL]** + xm\_tr  
**[FAIL]** + fcm  
**[FAIL]** ERROR: strict validation fails naked dummy tasks

Do you know why it is failing? I don’t have much confidence in my changes, so please let me know what I forgot to add.

Thanks,

Ayesha

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [26 October 2022 15:56 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/32 "2022-10-26T15:56:12Z")

</div>

Hi Ayesha:  
That sounds like good progress! I suspect you might have a typo or something in your rose-suite.conf file or in your suite.rc file. This is based upon your error messages that say:

```auto
[FAIL] + 21512
[FAIL] + AT_JULES_REVISION

```

I don’t have access to Monsoon currently. It might be a couple of weeks before I will have Monsoon access again. Can you check your changes to your suite into the MOSRS archive? Then I could look at them. If you could do your work on JASMIN instead of Monsoon, I could help you much more.  
Patrick

---

<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [27 October 2022 12:48 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/33 "2022-10-27T12:48:06Z")

</div>

Hi Patrick,

I’m committed my changes: [https://code.metoffice.gov.uk/trac/roses-u/browser/c/p/9/7/6/trunk/](https://code.metoffice.gov.uk/trac/roses-u/browser/c/p/9/7/6/trunk/)

I’ve also tried running this suite on JASMIN and I’m getting the same FAIL messages as I do on Monsoon. So I think it’s successfully ported but I’ll keep looking at it.

Thanks,

Ayesha

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [27 October 2022 15:33 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/34 "2022-10-27T15:33:05Z")

</div>

Hi Ayesha:  
I updated your `u-cp976` suite. The new update is `u-cr679`.

It was missing a `site/suite.rc.MONSOON` or `site/suite.rc.CEDA_JASMIN`; I copied the one from `u-al752` for `site/suite.rc.CEDA_JASMIN` .

Also, the `[scheduling] `section was a bit complicated for me to quickly understand, so I replaced the `[scheduling]` section with what was in `u-al752`. I had to put the `JULES` string in lower case (`jules`) in the `[scheduling]` section, in order to match the `[[jules]]` section of `[runtime]`. Otherwise, it complained when I did `rose suite-run`.

For JASMIN, we also need to use the `JULES_FCM='fcm:jules.x_tr'` instead of `JULES_FCM='fcm:jules.xm_tr'`  
You can see this change mentioned in Step #10 of:

> **[Tutorial for setting up Rose/Cylc in order to run JULES on CEDA JASMIN - Land...](https://research.reading.ac.uk/landsurfaceprocesses/software-examples/tutorial-rose-cylc-jules-on-jasmin/)**
>
> Tutorial for setting up Rose/Cylc in order to run JULES on CEDA JASMIN     (last updated 19 July 2022) First, complete the JASMIN setup at the following site: https://help.jasmin.ac.uk/category/158-getting-started...Read More \>

It looks like it’s building now on JASMIN. The `fcm_make` app is running. And there are some `jules` apps and the `make_plots` app that are waiting to run. It still might need further fixing, but maybe one step has been taken forward.

Patrick

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [31 October 2022 09:22 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/35 "2022-10-31T09:22:00Z")

</div>

Hi Ayesha:  
How is it working now?  
Patrick

---

<div class="post-metadata">

**Author:** ![ash221](https://avatars.discourse-cdn.com/v4/letter/a/ed8c4c/32.png) [@ash221](https://cms-helpdesk.ncas.ac.uk/u/ash221)\
**Post date:** [31 October 2022 09:29 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/36 "2022-10-31T09:29:40Z")

</div>

Hi, it ran perfectly when build=true and skip\_spinup=false, but didn’t work when build=false. I think it was something to do with scheduling so I’m trying it again now (it says ‘submitted’ and has done for a while, so I think there’s a queue this morning). Thank you so much for helping out so much!!! I really appreciate it.

---

<div class="post-metadata">

**Author:** ![pmcguire](https://avatars.discourse-cdn.com/v4/letter/p/b782af/32.png) [@pmcguire](https://cms-helpdesk.ncas.ac.uk/u/pmcguire)\
**Post date:** [31 October 2022 13:15 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/37 "2022-10-31T13:15:52Z")

</div>

Hi Ayesha:  
I am glad it works with build=true. Are you running it first with build=true, before trying to modify the suite and then running it with build=false?

Also, once the `fcm_make` successfully runs and maybe the `jules` app fails somewhere, you can just make changes to the `jules` app, run `rose suite-run --reload` (and maybe a `rose sgc` if there is no GUI), and then retrigger the `jules` app without retriggering the successful `fcm_make` app.

Patrick

---

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**Author:** ![system](https://europe1.discourse-cdn.com/flex013/uploads/cms_support/original/1X/1fd2411499ffcbc299fe756cd5cdf26e44956558.png) [@system](https://cms-helpdesk.ncas.ac.uk/u/system)\
**Post date:** [30 November 2022 13:16 UTC](https://cms-helpdesk.ncas.ac.uk/t/updating-suite-u-cp976/735/38 "2022-11-30T13:16:46Z")

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