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GambitBSM / gambit_2.0

GAMBIT: The Global and Modular Beyond-the-Standard-Model Inference Tool
https://gambit.hepforge.org
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Gambit segmentation fault #1

Open aseshkdatta opened 3 years ago

aseshkdatta commented 3 years ago

Hi,

The example mpirun of gambit as suggested on page 21 of the GUM paper on arXiv (2107.00030) is leading to segmentation fault on a particular (desktop) machine. The message is as follows.

Could you please help.

Thanks and regards. Asesh

================================================= asesh@albert:~/MyPlace/Packages/gambit_2.0$ time mpirun -n 4 gambit -f yaml_files/MDMSM_Tute.yaml

GAMBIT 2.0.0 http://gambit.hepforge.org

GAMBIT 2.0.0 http://gambit.hepforge.org

GAMBIT 2.0.0 http://gambit.hepforge.org

GAMBIT 2.0.0 http://gambit.hepforge.org

mpirun noticed that process rank 3 with PID 0 on node albert exited on signal 11 (Segmentation fault).

real 0m5.359s user 0m6.412s sys 0m0.089s asesh@albert:~/MyPlace/Packages/gambit_2.0$

patscott commented 3 years ago

Hi Asesh,

@tegonzalo has been on holiday but I think he'll be back online at the start of next week and might be able to help out. In the meantime, can you try installing a different MPI library please, and also posting the the log files so that we can see where the segmentation fault seems to have occurred?

Thanks - Pat

aseshkdatta commented 3 years ago

Hi Pat,

Thank you so much for the information and for your suggestion. Right now, I am working with our computer admin on the issue and is going to take up soon what you have suggested.

Cheers. Asesh

Hi Asesh,

@tegonzalo has been on holiday but I think he'll be back online at the start of next week and might be able to help out. In the meantime, can you try installing a different MPI library please, and also posting the the log files so that we can see where the segmentation fault seems to have occurred?

Thanks - Pat

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-888809191

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Hi Pat,

Just a curiosity.... can it be a memory (swap) related issue as some pages on the internet suggest?

I am for sure working on a low memory (for the purpose) machine (8 GB RAM with 16 GB swap).

However, with the same availability/allocation of memory on another machine, the test 'mpirun' of Gambit went smooth. With this in mind, your suggestion to use a different MPI library appears crucial.

Cheers. Asesh

Hi Pat,

Thank you so much for the information and for your suggestion. Right now, I am working with our computer admin on the issue and is going to take up soon what you have suggested.

Cheers. Asesh

Hi Asesh,

@tegonzalo has been on holiday but I think he'll be back online at the start of next week and might be able to help out. In the meantime, can you try installing a different MPI library please, and also posting the the log files so that we can see where the segmentation fault seems to have occurred?

Thanks - Pat

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-888809191

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Hi Pat,

Even a serial run on this machine is returning the following.

===================================== @.***:~/MyPlace/Packages/gambit_2.0$ ./gambit -f yaml_files/MDMSM_Tute.yaml

GAMBIT 2.0.0 http://gambit.hepforge.org

Segmentation fault (core dumped) @.***:~/MyPlace/Packages/gambit_2.0$

Anything else to worry about before we go for a different MPI library?

Cheers. Asesh

Hi Asesh,

@tegonzalo has been on holiday but I think he'll be back online at the start of next week and might be able to help out. In the meantime, can you try installing a different MPI library please, and also posting the the log files so that we can see where the segmentation fault seems to have occurred?

Thanks - Pat

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-888809191

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

patscott commented 3 years ago

In that case, please re-cmake and re-compile with MPI support completely turned off (-DWITH_MPI=OFF), confirm that you still still get the error, and send us the single log from that run. It seems like the issue is probably some other library (not MPI). I think it unlikely that it is memory related, as GAMBIT takes much less memory to run than to compile.

aseshkdatta commented 3 years ago

Thanks a lot, Pat. I'll soon try that out.

Cheers. Asesh

In that case, please re-cmake and re-compile with MPI support completely turned off (-DWITH_MPI=OFF), confirm that you still still get the error, and send us the single log from that run. It seems like the issue is probably some other library (not MPI). I think it unlikely that it is memory related, as GAMBIT takes much less memory to run than to compile.

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-889057612

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Hi,

Should I use "-DWITH_MPI=OFF" when building GUM or I should build Gambit itself with this option first?

Also, when I face the following message due to a previous `make', how should I proceed; simply proceed pressing 'enter'?

@.***:~/Packages/gambit_2.0/build$ make micromegas_MDMSM [ 0%] Built target check-rebuild-.micromegas_3.6.9.2_base [ 0%] Performing patch step for '.micromegas_3.6.9.2_base' patching file CalcHEP_src/c_source/chep_crt/Makefile Reversed (or previously applied) patch detected! Assume -R? [n]

Thanks. Asesh

In that case, please re-cmake and re-compile with MPI support completely turned off (-DWITH_MPI=OFF), confirm that you still still get the error, and send us the single log from that run. It seems like the issue is probably some other library (not MPI). I think it unlikely that it is memory related, as GAMBIT takes much less memory to run than to compile.

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-889057612

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Hi Pat,

I rebuilt both Gambit and GUM with re-cmake (with -DWITH_MPI=OFF at all stages) and re-make.

The problem remains (please see below).

@.***:~/Packages/gambit_2.0$ ./gambit -f yaml_files/MDMSM_Tute.yaml

GAMBIT 2.0.0 http://gambit.hepforge.org

Segmentation fault (core dumped) @.***:~/Packages/gambit_2.0$

I did not quite understand which log file you meant by "single log from that run". I am attaching herewith the following two log files. ./build/CMakeFiles/CMakeError.log ./build/CMakeFiles/CMakeOutput.log (Similar log files under the same names are found in ./gum/build/CMakeFiles/CMakeError.log ./gum/build/CMakeFiles/CMakeOutput.log)

Please let me know if you were looking for a different log/output.

Thanks. Asesh

PS: I noted that on my laptop, where gambit ran smoothly with mpirun, "CMakeError.log" have similar (error) contents!

In that case, please re-cmake and re-compile with MPI support completely turned off (-DWITH_MPI=OFF), confirm that you still still get the error, and send us the single log from that run. It seems like the issue is probably some other library (not MPI). I think it unlikely that it is memory related, as GAMBIT takes much less memory to run than to compile.

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-889057612

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

patscott commented 3 years ago

Also, when I face the following message due to a previous `make', how should I proceed; simply proceed pressing 'enter'?

This one indicates that something has gone wrong in the download or build of micromegas. In this case you need to nuke micromegas and try building it again: nuke micromegas_MDMSM; make micromegas_MDMSM.

As to the logs, what I mean is the default log in the output directory of the GAMBIT run that you are trying to launch, i.e runs/MDMSM/logs/default.log. If that doesn't exist, then please send scratch/default.log.

To attach files, I think you need to log into GitHub (the ones you apparently attached by email don't seem to have come through).

aseshkdatta commented 3 years ago

Thanks a lot, Pat.

I'll get back to you soon.

Cheers. Asesh

Also, when I face the following message due to a previous `make', how should I proceed; simply proceed pressing 'enter'?

This one indicates that something has gone wrong in the download or build of micromegas. In this case you need to nuke micromegas and try building it again: `nuke micromegas_MDMSM; make micromegas_MDMSM'.

As to the logs, what I mean is the default log in the output directory of the GAMBIT run that you are trying to launch, i.e runs/MDMSM/logs/default.log'. If that doesn't exist, then please send scratch/default.log`.

To attach files, I think you need to log into GitHub (the ones you apparently attached by email don't seem to have come through).

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-889585804

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Thanks a lot for the suggestions. I am writing below.

As to the logs, what I mean is the default log in the output directory of the GAMBIT run that you are trying to launch, i.e runs/MDMSM/logs/default.log'. If that doesn't exist, then please send scratch/default.log`.

==> No 'runs' folder is created under gambit home. A 'scratch' folder is found which contains two sub-folder: 'build_time' and 'run_time', none of which contains anything inside.

To attach files, I think you need to log into GitHub (the ones you apparently attached by email don't seem to have come through).

==> Attaching a screen-shot of the run showing the subsequent folder details.

Please observe and kindly suggest me how to proceed.

Regards. Asesh

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-889585804

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Hi,

I am so sorry. By mistake, I attached the screenshot with my previous mail. I am attaching it on the github gambit page.

Regards. Asesh

Thanks a lot for the suggestions. I am writing below.

As to the logs, what I mean is the default log in the output directory of the GAMBIT run that you are trying to launch, i.e runs/MDMSM/logs/default.log'. If that doesn't exist, then please send scratch/default.log`.

==> No 'runs' folder is created under gambit home. A 'scratch' folder is found which contains two sub-folder: 'build_time' and 'run_time', none of which contains anything inside.

To attach files, I think you need to log into GitHub (the ones you apparently attached by email don't seem to have come through).

==> Attaching a screen-shot of the run showing the subsequent folder details.

Please observe and kindly suggest me how to proceed.

Regards. Asesh

-- You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-889585804

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Screenshot from 2021-07-30 16-48-01

aseshkdatta commented 3 years ago

Attached the mentioned screen-shot. Thanks.

patscott commented 3 years ago

Hi Asesh - OK, maybe we should start with your full cmake output. In your build dir, please run

make nuke-all
rm -rf *
cmake [your cmake options] ...

and post the output here.

aseshkdatta commented 3 years ago

Hi Pat,

Thanks a lot.

After executing "make nuke-all" and "rm -rf *" from the "build" dir, I ran "cmake -DWITH_MPI=OFF .." as suggested by you earlier. cmake-log1.txt

I am attaching herewith the output of cmake. Asesh

tegonzalo commented 3 years ago

Hi Asesh,

Apologies for the silence, I was on holidays. Thanks Pat for taking over.

I am attaching herewith the output of cmake.

Your cmake output seems fine. MPI is correctly disabled and everything else seems to have configured correctly. Please build now gambit and the relevant backends like this

make micromegas_MDMSM
make calchep
make -j<n> gambit

Once that is finished, if there are no errors, then run a simple test run, first using the spartan yaml file, i.e.

./gambit -f yaml_files/spartan.yaml

and if that works, then run the MDMSM.yaml file.

After every scan, a corresponding folder should have been created in the runs directory, e.g. runs/spartan, with logs, samples and scanner info. If any of the scans above fail but you still have the logs in that directory, please send them so we can have a look at it.

Cheers, Tomas

aseshkdatta commented 3 years ago

Hi Tomas,

Thanks for the mail.

It seems the "runs" folder itself is not being created even as the Gambit run ends up in seg fault. Please see below.

asesh@albert:~/Packages/gambit_2.0$ ./gambit -f yaml_files/spartan.yaml

GAMBIT 2.0.0 http://gambit.hepforge.org

Segmentation fault (core dumped) asesh@albert:~/Packages/gambit_2.0$

Please let me know how to proceed under the circumstances.

Cheers. Asesh

tegonzalo commented 3 years ago

That is really unusal. And you said that there is nothing either on scratch/run_time, right? Could you run the following commands and tell me what you see?

First just do

./gambit

If everything is fine, that should print usage instructions, but it requires creating the scratch files, so you will probably see the segfault too. After that also do

./gambit modules

which should give you the list of built modules, but again, may fail if the problem is due to the scratch files.

Let me know what you see on both cases.

Thanks for you help!

Tomas

aseshkdatta commented 3 years ago

You are welcome, Tomas. The exercise is also very much helpful to me. Here is what I see.

asesh@albert:~/Packages/gambit_2.0$ asesh@albert:~/Packages/gambit_2.0$ ./gambit

GAMBIT 2.0.0 http://gambit.hepforge.org

Segmentation fault (core dumped) asesh@albert:~/Packages/gambit_2.0$ asesh@albert:~/Packages/gambit_2.0$ asesh@albert:~/Packages/gambit_2.0$ ./gambit modules

GAMBIT 2.0.0 http://gambit.hepforge.org

Segmentation fault (core dumped) asesh@albert:~/Packages/gambit_2.0$

Cheers. Asesh

aseshkdatta commented 3 years ago

Right; "scratch/run_time" folder has nothing created inside it!

Asesh

aseshkdatta commented 3 years ago

Dear Tomas,

Could you have a look into the issue? Kindly share your observations.

Cheers. Asesh

That is really unusal. And you said that there is nothing either on scratch/run_time, right? Could you run the following commands and tell me what you see?

First just do

./gambit

If everything is fine, that should print usage instructions, but it requires creating the scratch files, so you will probably see the segfault too. After that also do

./gambit modules

which should give you the list of built modules, but again, may fail if the problem is due to the scratch files.

Let me know what you see on both cases.

Thanks for you help!

Tomas

-- You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-891139542

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

tegonzalo commented 3 years ago

Hi Asesh,

I've been trying to figure out what could be happening to produce a segfault that early on the run, because it doesn't make sense as this has never happened before. Could you show me the backtrace of the segfault? Launch the debugger

gdb ./gambit

and then inside the debugger just run 

r modules

once you get the segfault then write

backtrace

and show me what you get.

tegonzalo commented 3 years ago

Also run

r models

just to make sure it has nothing to do with the yaml reader

Thanks again for your help in resolving this.

aseshkdatta commented 3 years ago

Thanks, Tomas. Here I am attaching the output.

Asesh backtrace-1

aseshkdatta commented 3 years ago

Hi Tomas,

Does it look like a Mathematica WSTP issue?

You may perhaps remember (shared with Pat also a few weeks ago) that there was an issue with the shared WSTP library (broken) on Mathematica 10 which I am having on the present computer.

To circumvent that I replaced the entry "libWSTP64i4.so" in the file "build/CMakeCache.txt" file by "libWSTP64i4.a" as shown below.

//WSTP library to link against. Mathematica_WSTP_LIBRARY:FILEPATH=/usr/local/Wolfram/Mathematica/10.0/SystemFiles/Links/WSTP/DeveloperKit/Linux-x86-64/CompilerAdditions/libWSTP64i4.a

The build went smoothly with this replacement and I was asked to post this solution on github. However, since I couldn't yet run gambit successfully, I postponed posting the solution.

Kindly take a close look into this aspect as well.

Cheers. Asesh

Also run

r models

just to make sure it has nothing to do with the yaml reader

Thanks again for your help in resolving this.

-- You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-893371638

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

tegonzalo commented 3 years ago

Ah, yes, it is definitely a Mathematica issue. Fortunately to run gambit you don't need Mathematica, you only need it to run gum. So when compiling gambit you could do 

cmake -Ditch="Mathematica" ..

and then you can recompile with make and try running it. With this you will (hopefully) get gambit working.

aseshkdatta commented 3 years ago

Okay, Tomas. Let me try it out by ditching Mathematica.

Will let you know. Asesh

Ah, yes, it is definitely a Mathematica issue. Fortunately to run gambit you don't need Mathematica, you only need it to rum gum. So when compiling gambit you could do

cmake -Ditch="Mathematica" ..

and then you can recompile with make and try running it. With this you will (hopefully) get gambit working.

-- You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-893436070

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

aseshkdatta commented 3 years ago

Right, Tomas. By ditching Mathematica, gambit runs without a segfault. But, as you say, I cannot build gum.

Could you suggest a work-around with Mathematica 10 so that I could keep it in the build process and thereof successfully work with gum.

As we find, my earlier naive fix of replacing the shared WSTP library with its static counterpart didn't finally help!

Thanks. Asesh

Ah, yes, it is definitely a Mathematica issue. Fortunately to run gambit you don't need Mathematica, you only need it to rum gum. So when compiling gambit you could do

cmake -Ditch="Mathematica" ..

and then you can recompile with make and try running it. With this you will (hopefully) get gambit working.

-- You are receiving this because you modified the open/close state. Reply to this email directly or view it on GitHub: https://github.com/GambitBSM/gambit_2.0/issues/1#issuecomment-893436070

============================= AseshKrishna Datta Professor 'H' Theoretical High Energy Physics Group Harish-Chandra Research Institute (HRI) (Department of Atomic Energy, Govt. of India) Allahabad (Prayagraj) UP INDIA 211019

tegonzalo commented 3 years ago

I think it's because you are changing the location of the library in CMakeCache.txt. That file is automatically generated when you run cmake, so any changes to that file will be ignored. But your suggestion of using the static library should work anyway, you just need to pass it as a cmake flag. So when building gum run

cmake -DMathematica_WSTP_LIBRARY=<path_to_your_ibWSTP64i4.a> ..

and then make gum with make.

aseshkdatta commented 3 years ago

Hi Tomas,

Thanks for your observations.

Using "cmake -Ditch="Mathematica" .. " during gambit build and employing

cmake -DMathematica_WSTP_LIBRARY=/usr/local/Wolfram/Mathematica/10.0/SystemFiles/Links/WSTP/DeveloperKit/Linux-x86-64/CompilerAdditions/libWSTP64i4.a ..

during gum build, I end up with the following error message of mpirun of gambit. Segfault is not appearing though any more.

I followed the directives given in the bottom of the right column on page 19 of arXiv:2107.00030 for the MDMSM model and hence only built "micromegas_MDMSM", "calchep", "gamlike" and "ddcalc". The message is talking about DarkSUSY.

Could you please shed some light.

Thanks. Asesh gambit-MDMSM-log.txt

tegonzalo commented 3 years ago

That seems to imply that you need to also build darksusy. I don't think that is intended, as you already have micromegas. Let me investigate further. But if you want to continue with the testing, just make

make darksusy_generic_wimp
pstoecker commented 3 years ago

According to the version of MDMSM_Tute.yaml that made it to version 2.0.0 of gambit, it is intended as the function SimYieldTable_DarkSUSY is chosen to fulfil the capability SimYieldTable for the gamma ray yields that are required by lnL_FermiLATdwarfs.

It might be a typo and it should be SimYieldTable_MicrOmegas. In that case there should be no need for darksusy as far as I see it.

tegonzalo commented 3 years ago

Yes, I just figure out that myself too. @aseshkdatta please just change SimYieldTable_DarkSUSY for SimYieldTable_MicrOmegas in MDMSM_Tute.yaml and try with that.

I will modify that on master so that it gets out in the next release

aseshkdatta commented 3 years ago

Hi, it's giving an error saying

Error reading Inifile "yaml_files/MDMSM_Tute.yaml"! Please check that file exist! (yaml-cpp error: yaml-cpp: error at line 127, column 17: illegal map value )

Attaching the full message herewith.

Asesh gambit-run-yaml-file-with-SimYieldTable_MicrOmegas.txt

tegonzalo commented 3 years ago

Can you send the yaml file so that I can see where the error is?

aseshkdatta commented 3 years ago

Here is the yaml file. I added ".txt" extension so that it can be uploaded to this page.

Asesh

MDMSM_Tute.yaml.txt

tegonzalo commented 3 years ago

Ok, in line 127 you need to make sure that the indentations match. So function should just fall below capability, but just using spaces, not tabs.

aseshkdatta commented 3 years ago

Thanks for pointing that out. I corrected that and ran gambit again. The error message looks like the following. The detailed one is attached herewith.

Asesh

/home/asesh/Packages/gambit_2.0/Backends/installed/calchep/3.6.27/sbin/newProcess: 87: exit: Illegal number: -1 Likelihood contribution from DarkBit::lnL_oh2_upperlimit: -196.799 Likelihood contribution from DarkBit::LUX_2016_GetLogLikelihood: -1.46732 Likelihood contribution from DarkBit::XENON1T_2018_GetLogLikelihood: -3.64953 PROCESS: ~chi,~chi -> mu+,mu- This particle is absent in the model Can not compile ~chi,~chi -> mu+,mu- [albert:09020] Process received signal [albert:09020] Signal: Segmentation fault (11) [albert:09020] Signal code: Address not mapped (1) [albert:09020] Failing at address: 0x28 [albert:09020] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x12980)[0x7f184caa7980] [albert:09020] [ 1] /home/asesh/Packages/gambit_2.0/Backends/installed/calchep/3.6.27/lib/libcalchep.so(passParameters+0x73)[0x7f17bd6b1fdf] [albert:09020] [ 2] gambit(+0x15ecb18)[0x55f206ebbb18] gambit-run-corrected-yaml-file-SimYieldTable_MicrOmegas.txt

tegonzalo commented 3 years ago

It looks like something is wrong with calchep. Please try nuking it and rebuilding it again

make nuke-calchep
make calchep
aseshkdatta commented 3 years ago

Thanks, Tomas. Do I need to make gambit after that?

Asesh

tegonzalo commented 3 years ago

No, just calchep this time

aseshkdatta commented 3 years ago

Here is the error message:

theta12: 0.58376
theta13: 0.15495
theta23: 0.76958

nuclear_params_sigmas_sigmal: deltad: -0.427 deltas: -0.085 deltau: 0.842 sigmal: 58 sigmas: 43

Raised at: line 74 in function void Gambit::BackendIniBit::CalcHEP_3_6_27_init() of /home/asesh/Packages/gambit_2.0/Backends/src/frontends/CalcHEP_3_6_27.cpp. rank 1: FinalizeWithTimeout failed to sync for clean MPI shutdown, calling MPI_Abort... rank 1: Issuing MPI_Abort command, attempting to terminate all processes...

MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them.

rank 2: FinalizeWithTimeout failed to sync for clean MPI shutdown, calling MPI_Abort... rank 2: Issuing MPI_Abort command, attempting to terminate all processes... [albert:11423] 1 more process has sent help message help-mpi-api.txt / mpi-abort [albert:11423] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages

tegonzalo commented 3 years ago

Can you send me the default log? (runs/MDMSM/logs/default.log)

aseshkdatta commented 3 years ago

All 4 of them? Or one will suffice?

Asesh

tegonzalo commented 3 years ago

From your message above, it looks like rank 1 was the one that found the error, so send me rank 1

aseshkdatta commented 3 years ago

Here it is.... default.log_1.txt