make mpis error

[Markus Ruhsam]

Hello,

I am trying to install the parallel version of migrate-n on an Ubuntu 18.04.3 LTS server. After installing openmpi-4.0.1 without any obvious error messages I installed migrate-n 4.4.4, using ./configure and 'make clean' without any error. However, 'make mpis' throws up a zlib error that showgit.sh isn't found (see screenshot below).

Any ideas what the problem is/

Thanks for your help

Markus

[Peter Beerli]

Hi Markus,

the wrnings about missing showgit.sh and the message about zlib are not the culprit, 

your MPI installation is probably incomplete, 

check out this answer:

https://askubuntu.com/questions/738667/problem-with-mpicc

I assume that your path for the libraries is not set, other users did not install all the openmpi parts

to compile and run migrate-n-mpi you will need

the openmpi developer and runtime libraries

check out this document: http://lsi.ugr.es/jmantas/pdp/ayuda/datos/instalaciones/Install_OpenMPI_en.pdf

I am sure you will need at least something like this and a working C/C++ compiler:

0. sudo apt-get install openmpi-bin libopenmpi-dev 

Peter

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[Markus Ruhsam]

Hi Peter,

I've run the command sudo apt-get install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3
libopenmpi-dbg libopenmpi-dev as outlined in the OpenMPI document and also sudo apt-get install openmpi-bin libopenmpi-dev as you suggested. Then running the 'make mpis' command still resulted in the same error as before (about missing showgit) and running 'mpirun -np 4 migrate-n-mpi parmfile.twoswisstowns' in the example folder started off promising but then gave this SEVERE ERROR message (see screenshot below). Does this give you a hint at what's missing?

Thanks

Markus

On Wednesday, February 5, 2020 at 3:20:04 PM UTC, Peter wrote:

Hi Markus,

the wrnings about missing showgit.sh and the message about zlib are not the culprit, 

your MPI installation is probably incomplete, 

check out this answer:

https://askubuntu.com/questions/738667/problem-with-mpicc

I assume that your path for the libraries is not set, other users did not install all the openmpi parts

to compile and run migrate-n-mpi you will need

the openmpi developer and runtime libraries

check out this document: http://lsi.ugr.es/jmantas/pdp/ayuda/datos/instalaciones/Install_OpenMPI_en.pdf

I am sure you will need at least something like this and a working C/C++ compiler:

0. sudo apt-get install openmpi-bin libopenmpi-dev 

Peter

On Feb 5, 2020, at 7:28 AM, 'Markus Ruhsam' via migrate-support <migrate...@googlegroups.com> wrote:

Hello,

I am trying to install the parallel version of migrate-n on an Ubuntu 18.04.3 LTS server. After installing openmpi-4.0.1 without any obvious error messages I installed migrate-n 4.4.4, using ./configure and 'make clean' without any error. However, 'make mpis' throws up a zlib error that showgit.sh isn't found (see screenshot below).

Any ideas what the problem is/

Thanks for your help

Markus

<Auto Generated Inline Image 1.png>

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[Peter Beerli]

I will need to see the complete configure and make mpis

log, the error you show should not happen, the missing showgit.sh is not part problem.

Are node1 and node2 different computers or different cores on your single computer.

Peter

On Feb 7, 2020, at 10:32 AM, 'Markus Ruhsam' via migrate-support <migrate...@googlegroups.com> wrote:

Hi Peter,

I've run the command sudo apt-get install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3
libopenmpi-dbg libopenmpi-dev as outlined in the OpenMPI document and also sudo apt-get install openmpi-bin libopenmpi-dev as you suggested. Then running the 'make mpis' command still resulted in the same error as before (about missing showgit) and running 'mpirun -np 4 migrate-n-mpi parmfile.twoswisstowns' in the example folder started off promising but then gave this SEVERE ERROR message (see screenshot below). Does this give you a hint at what's missing?

Thanks

Markus

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[Markus Ruhsam]

config.log and mpis_log attached.

Thanks for looking into this

Markus

[Peter Beerli]

Markus,

the config.log looks fine to me

Ignore the warning messages in the mpis_log.txt, they only address missing return values

for the scanf and fscanf functions, but these return values are there only to count errors.

On other systems (my mac) I get warnings for catching those return values if I do not use later.

Not clear what happened but could you run the content of this folder:

Peter

P.S. on my system I ran: mpirun -np 9 —oversubscribe migrate-n-mpi parmfile.twotowns -nomenu

without any problem.

[Markus Ruhsam]

I extracted the two files from the testfolder and ran your command "mpirun -np 9 —oversubscribe migrate-n-mpi parmfile.twoswisstowns -nomenu" which resulted in 'can't find the executable file'

Running the simplified command "mpirun -np 9 migrate-n-mpi parmfile.twoswisstowns" started off with the migrate-n input page and after typing Y it ran for a bit but then came up with the severe error message again:

Markus

[Peter Beerli]

OK,

this did not help, could you try this below and if that fails the next suggestion:

cp twoswisstowns infile

mpirun -np 3 migrate-n-mpi -nomenu

# this runs the default using the example, the parmfile for the example prints out the best tree which may have a problem on your machine

if this fails go back to the src:

make clean

make mpis-debug

# this will generate more warnings than the other compile, it will overwrite your migrate-n-mpi with a debug version

and then again

mpirun -np 3 migrate-n-mpi -nomenu

this will write lots of stuff to the screen

I will need the complete output that is written to the screen and the outfile fragment that is produced.

There is something special about your machine, but not clear what

Peter

On Feb 10, 2020, at 3:12 AM, 'Markus Ruhsam' via migrate-support <migrate...@googlegroups.com> wrote:

I extracted the two files from the testfolder and ran your command "mpirun -np 9 —oversubscribe migrate-n-mpi parmfile.twoswisstowns -nomenu" which resulted in 'can't find the executable file'

<Auto Generated Inline Image 1.png>

Running the simplified command "mpirun -np 9 migrate-n-mpi parmfile.twoswisstowns" started off with the migrate-n input page and after typing Y it ran for a bit but then came up with the severe error message again:

<Auto Generated Inline Image 2.png>

Markus

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[Peter Beerli]

Markus,

wait with checking, I have installed ubuntu and can generate the same error on my system, will hopefully have a fix soon;

Peter

P.S. the instructions I have earlier this morning will not work without editing the Makefile 

[Markus Ruhsam]

Hi Peter,

It's working! Using your first suggestion of  'cp twoswisstowns infile' and 'mpirun -np 3 migrate-n-mpi -nomenu' started off the process without any error and it's still running. However, it actually uses my paramfile and not the twoswisstowns. After I installed everything I never tried my own file but wanted to see whether everything was working okay using 'cd migrate-4.4.4/example' and 'mpirun -np 4 migrate-n-mpi parmfile.twoswisstowns'. Because these gave the above errors (and it still does...) I never tried 'mpirun -np 4 migrate-n-mpi parmfile' which is working just fine as I have just found out (as is 'mpirun -np 3 migrate-n-mpi -nomenu'). So the server just seems to take exception to the example file... Sorry about 'much ado about nothing'. By the way what does the -nomenu do?

Thanks very much for your help

Markus

[Markus Ruhsam]

UPDATE: I've just tried a different input file which was created the same way as the previous one (with PGDSpider) and got that SEVERE ERROR message again. So there's something funny going on... Hope that you can work out what the problem is.

[Peter Beerli]

Markus,

(1) the error is triggered by the option
print-tree=BEST:besttreefile
with that set to
print-tree=NO
it should work fine. But is yet unclear to me why this fails on ubuntu but works just fine on a mac.

(2) this may be a different problem, and related to the infile (send me the file: bee...@fsu.edu)

Peter

> On Feb 11, 2020, at 4:57 AM, 'Markus Ruhsam' via migrate-support <migrate...@googlegroups.com> wrote:
>
> UPDATE: I've just tried a different input file which was created the same way as the previous one (with PGDSpider) and got that SEVERE ERROR message again. So there's something funny going on... Hope that you can work out what the problem is.
>
>
>

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[Markus Ruhsam]

Hi Peter,

Thanks very much for this. I sent the files to your email address two days ago. Could you please let me know whether you got them?

Markus