[BUG/ISSUE] MAPL needs several dirty fixes (changing $VPATH, $CPATH) to compile

[geoschem]

[BUG/ISSUE] MAPL needs several dirty fixes (changing $VPATH, $CPATH) to compile

[JiaweiZhuang]

Those fixes are not needed at all on NASA Pleiades (uses SUSE Linux Enterprise Server 12). Compiles & runs smoothly after loading default modules and setting basic environment variables. Probably not surprising that NASA software works well on NASA computers :)

[lizziel]

Very interesting. Once the new MAPL is up and running, if these fixes are still needed in some cases we can add them in. I assume using the fixes with Odyssey/Pleiades also works even though they aren’t needed. True?

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-- Lizzie Lundgren Scientific Programmer GEOS-Chem Support Team [email protected]<mailto:[email protected]> http://wiki.geos-chem.org/GEOS-Chem_Support_Team Please direct all GEOS-Chem support issues to the entire GEOS-Chem Support Team at [email protected]<mailto:[email protected]>. This will allow us to serve you better. From: Jiawei Zhuang <[email protected]> Reply-To: geoschem/gchp <[email protected]> Date: Thursday, January 17, 2019 at 12:22 AM To: geoschem/gchp <[email protected]> Cc: Subscribed <[email protected]> Subject: Re: [geoschem/gchp] MAPL needs several dirty fixes (changing $VPATH, $CPATH) to compile (#17) Those fixes are not needed at all on NASA Pleiades (uses SUSE Linux Enterprise Server 12). Compiles & runs smoothly after loading default modules and setting basic environment variables. Probably not surprising that NASA software works well on NASA computers :) — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geoschem_gchp_issues_17-23issuecomment-2D455046461&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=xyVOGV-4mAPz62S8RZON4khwZesGKcGg2_BHL4y5NjQ&m=5nyvKqfsqSYcFNumo3Ze7rZNBmOoD_dgzgeNdkEAsrI&s=1JfY0oQA31MILrU11MR2q22VNByvuvaH9Yap5h2tdfQ&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAnyq3MCieQgzQr-2DO-2DspFfx8L33cyNRyks5vEAh2gaJpZM4Z6vPK&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=xyVOGV-4mAPz62S8RZON4khwZesGKcGg2_BHL4y5NjQ&m=5nyvKqfsqSYcFNumo3Ze7rZNBmOoD_dgzgeNdkEAsrI&s=dfo_8QtmzhOIYyXaVRmangEPWIjwD1RCZ6Q3VVsSIVA&e=>.

[JiaweiZhuang]

Just successfully compiled on CentOS 7 without all those fixes (on AWS, not Odyssey). Seems like an Ubuntu-only problem...

[lizziel]

Good to know. Thanks for reporting this. If you would like to test out compilation on Ubuntu with the new version of MAPL use GCHP branch MAPL_integration. I am curious about whether the fixes you had to apply before are still needed. If they are I can feed this back to GMAO in the near future.

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________________________________ From: Jiawei Zhuang <[email protected]> Sent: Thursday, March 7, 2019 8:17:28 PM To: geoschem/gchp Cc: Lundgren, Elizabeth W; Comment Subject: Re: [geoschem/gchp] MAPL needs several dirty fixes (changing $VPATH, $CPATH) to compile (#17) Just successfully compiled on CentOS 7 without all those fixes (on AWS, not Odyssey). Seems like an Ubuntu-only problem... — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geoschem_gchp_issues_17-23issuecomment-2D470766196&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=xyVOGV-4mAPz62S8RZON4khwZesGKcGg2_BHL4y5NjQ&m=fZACDWNA_J3TY6-OCjpZOD_EFJfIbJ2hJySLpQxGC1k&s=2YP3gkqTOTRdHTaksrUGhKeT5B7IOp6UUfdQsI7fN9U&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAnyqyq6TCiijredV5AHsH-2DAd-5FOAnx6Aks5vUboogaJpZM4Z6vPK&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=xyVOGV-4mAPz62S8RZON4khwZesGKcGg2_BHL4y5NjQ&m=fZACDWNA_J3TY6-OCjpZOD_EFJfIbJ2hJySLpQxGC1k&s=wyZcUCDoTb_F-B6Rw_7EJGmTNa91Xx7xOW2EPZnQqWg&e=>.

[lizziel]

@JiaweiZhuang Update to my last comment: To test out compilation on Ubuntu use GCHP branch MAPL_v1.0.0. Let us know if the MAPL dirty fixes for compilation on ubuntu are still required for the new version. If yes, I will discuss with GMAO. If no, I will close out this issue.

[JiaweiZhuang]

To test out compilation on Ubuntu use GCHP branch MAPL_v1.0.0.

Thanks! Which version/branch of GC-classic code should I use to match the MAPL_v1.0.0 branch?

[lizziel]

12.2.0.

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-- Lizzie Lundgren Senior Scientific Programmer GEOS-Chem Support Team [email protected]<mailto:[email protected]> http://wiki.geos-chem.org/GEOS-Chem_Support_Team Please direct all GEOS-Chem support issues to the entire GEOS-Chem Support Team at [email protected]<mailto:[email protected]>. This will allow us to serve you better. From: Jiawei Zhuang <[email protected]> Reply-To: geoschem/gchp <[email protected]> Date: Thursday, May 2, 2019 at 2:49 PM To: geoschem/gchp <[email protected]> Cc: "Lundgren, Elizabeth W" <[email protected]>, Comment <[email protected]> Subject: Re: [geoschem/gchp] MAPL needs several dirty fixes (changing $VPATH, $CPATH) to compile (#17) To test out compilation on Ubuntu use GCHP branch MAPL_v1.0.0. Thanks! Which version/branch of GC-classic code should I use to match the MAPL_v1.0.0 branch? — You are receiving this because you commented. Reply to this email directly, view it on GitHub<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_geoschem_gchp_issues_17-23issuecomment-2D488788059&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=xyVOGV-4mAPz62S8RZON4khwZesGKcGg2_BHL4y5NjQ&m=-QeGOFWnDEht6gUYmcJeZF93SzYX780frOtRg5FPFdQ&s=6baZfosnmd9a3LzdKvVDIb5N9jIo3d5qZD3vbM6jsWg&e=>, or mute the thread<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_AAE7FK64ZQEXIOVB3WPP4YTPTMZTHANCNFSM4GPK6PFA&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=xyVOGV-4mAPz62S8RZON4khwZesGKcGg2_BHL4y5NjQ&m=-QeGOFWnDEht6gUYmcJeZF93SzYX780frOtRg5FPFdQ&s=SJn7vY0BNg9ZpVw-gjF4uR8j4rbi7a4GhqFhFqbc6aU&e=>.

[lizziel]

@JiaweiZhuang What is the status of your planned test? The information I gave you is now outdated and dev/12.5.0 should be used instead, soon to be master.

[JiaweiZhuang]

OK I will test 12.5.0 instead.

[JiaweiZhuang]

Exact same problem with 12.3.2 (only on Ubuntu; no issue on CentOS). Will test 12.5.0 after the release.

[JiaweiZhuang]

Same problem for GCHP 12.5.0 (tested on Ubuntu). Here are two log files before and after the fix:

• compile_before_VPATH_fix.log
• compile_after_VAPTH_fix.log

In the first one you can see errors like:

c2c.F90:3:10: fatal error: MAPL_Generic.h: No such file or directory
    3 | #include "MAPL_Generic.h"
      |          ^~~~~~~~~~~~~~~~
compilation terminated.

In the second one those errors are gone. Although the compilation still fails due to #37.

[JiaweiZhuang]

GCHP 12.5.0 (even on CentOS) requires more CPATH/VPATH fixes than what's described on the top of this thread.

I've finally successfully compiled GCHP 12.5.0 (with gcc8.3.0 + OpenMPI3 + CentOS). Both the successful build and the failed builds can be reproduced by this Docker environment: https://github.com/JiaweiZhuang/docker_gchp/releases/tag/v0.1.0 (remove some fixes in Dockerfile and gchp.env to see how it fails).

1. First, the complier cannot find MAPL_Generic.h without this fix:

export CPATH=$GC_CODE_DIR/GCHP/Shared/MAPL_Base:$CPATH # MAPL_Generic.h

this was only needed on Ubuntu; don't know why CentOS also needs this starting 12.5.0.

2. Then, the build still fails at this newly-introduced PFIO module:

gmake[9]: *** No rule to make target `pfio_stringintegermapmod.mod', needed by `MAPL_IO.o'.  Stop.

Full log: compile_gchp12.5.0_fail_at_pfio.log

This can be fixed by

export VPATH=$GC_CODE_DIR/GCHP/Shared/GMAO_pFIO:$VPATH # pfio_stringintegermapmod.mod

3. Then, the build still fails at

gmake[8]: *** No rule to make target `m_set_eta.mod', needed by `AdvCore_GridCompMod.o'.  Stop.

Full log: compile_gchp12.5.0_fail_at_finding_eta.log

This can be fixed by

export VPATH=$GC_CODE_DIR/GCHP/Shared/GMAO_hermes:$VPATH # m_set_eta.mod

4. Then, the build still fails at

Fatal Error: Can't open module file 'm_set_eta.mod' for reading at (1): No such file or directory

Full log: compile_gchp12.5.0_fail_at_using_eta.log

This can be fixed by

ln -sf $GC_CODE_DIR/GCHP/Shared/GMAO_hermes/m_set_eta.mod $GC_CODE_DIR/GCHP/FVdycoreCubed_GridComp/

See this commit for all the above fixes: JiaweiZhuang/docker_gchp@d40b0c4

5. Finally, because of geoschem/GCHP#39 (comment), the build still fails at

/usr/bin/ld: cannot find -lblas
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lGMAO_hermes

Full log: compile_gchp12.5.0_fail_at_blas.log

This can be fixed by yum install -y lapack-devel blas-devel (JiaweiZhuang/docker_gchp@e3c617d)

6. Then we finally got this successful build: compile_gchp12.5.0_success.log

For comparison, GCHP 12.3.2 can be built successfully without any of the above fixes (on CentOS) . Full log: compile_gchp12.3.2_success.log
(However, GCHP 12.3.2 cannot be used with gfortran due to run-time errors like #15; I guess 12.5.0 is supposed to fix those run-time errors.)

[lizziel]

I am closing this issue since 13.0.0 will be leaps and bounds beyond 12.3.2 in the MAPL version. We are not updating old MAPL at this point. Issues encountered with MAPL in 13.0.0 should be submitted as new issues.