Re: error compiling gadget

From: Cynthia Saad (Student) <"Cynthia>
Date: Tue, 5 Dec 2017 10:48:21 +0000

i finally was able to run gadget2. when trying to compiling NGenic, i edited the makefile the same way it worked with Gadget. yet i am getting the same as i was getting when i was mistakingly using fftw3.



crs07_at_cynthiasubuntu:~/Downloads/N-GenIC$ make
mpicc -DNO64BITID -O3 -march=x86-64 -Wall -g -I/home/crs07/fftw2/include -I/home/crs07/gsl/include -c -o main.o main.c
main.c:3:24: fatal error: drfftw_mpi.h: No such file or directory
 #include <drfftw_mpi.h>
                        ^
compilation terminated.
<builtin>: recipe for target 'main.o' failed
make: *** [main.o] Error 1

thank you for bearing my questions!

________________________________
From: Antonio Bibiano <antbbn_at_gmail.com>
Sent: Wednesday, November 29, 2017 2:11:38 PM
To: Gadget General Discussion
Subject: Re: [gadget-list] error compiling gadget

Glad it worked,
Seems like you installed gsl in a non-standard directory, you can either try using your system tools to install the libgsl package or specifying the library path before running Gadget, something like this: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/crs07/fftw2/lib
And then ./Gadget2

Cheers,
Antonio

On Wed 29. Nov 2017 at 13:06, Cynthia Saad (Student) <crs07_at_mail.aub.edu<mailto:crs07_at_mail.aub.edu>> wrote:

THANK YOU! it didn't occur to me that i should be using the older version of fttw.

i successfully compiled the code.

when trying to run one of the examples i am getting

./Gadget2: error while loading shared libraries: libgsl.so.23: cannot open shared object file: No such file or directory


even though i have libgsl.so.23 in home/crs07/fftw2/lib, and in the makefile i put FFTW_LIBS= -L/home/crs07/fftw2/lib.


what am i doing wrong?

thank you so much for your help!!

________________________________
From: Antonio Bibiano <antbbn_at_gmail.com<mailto:antbbn_at_gmail.com>>
Sent: Tuesday, November 28, 2017 11:56:20 AM

To: Gadget General Discussion
Subject: Re: [gadget-list] error compiling gadget
You should use fftw2 to compile gadget.

You can find it here http://www.fftw.org/download.html<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.fftw.org%2Fdownload.html&data=02%7C01%7Ccrs07%40mail.aub.edu%7Cacf303c7a9f54b2ba30408d53646a7c6%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636474599462421928&sdata=v4HqNmj80btRVOtEVpSqfLDrsyMpLnTrd%2F2GNu7AAIA%3D&reserved=0>
Under "fftw 2.1.5"

Then follow the instructions provided by Jared.

Also the gadget guide (http://wwwmpa.mpa-garching.mpg.de/gadget/users-guide.pdf<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwwwmpa.mpa-garching.mpg.de%2Fgadget%2Fusers-guide.pdf&data=02%7C01%7Ccrs07%40mail.aub.edu%7Cacf303c7a9f54b2ba30408d53646a7c6%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C1%7C636474599462421928&sdata=UtHTkWnKMLOqU3yedZDHh0FEuF102fSpyhOMKQSwVBM%3D&reserved=0> , page 4) explains the options needed to compile it.

Cheers,
Antonio

On Tue 28. Nov 2017 at 10:11, Cynthia Saad (Student) <crs07_at_mail.aub.edu<mailto:crs07_at_mail.aub.edu>> wrote:

Hello

i'm really sorry, but i am still stuck with this. i was following this http://wwwmpa.mpa-garching.mpg.de/gadget/gadget-list/0171.html<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwwwmpa.mpa-garching.mpg.de%2Fgadget%2Fgadget-list%2F0171.html&data=02%7C01%7Ccrs07%40mail.aub.edu%7Cacf303c7a9f54b2ba30408d53646a7c6%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636474599462421928&sdata=bvcDWlIJ%2F%2FWQG2axKeeqU6VDgG0PF0RJB3Nf990AKwg%3D&reserved=0>

Re: Illegal Instruction error ... from Yves Revaz on 2007 ...<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwwwmpa.mpa-garching.mpg.de%2Fgadget%2Fgadget-list%2F0171.html&data=02%7C01%7Ccrs07%40mail.aub.edu%7Cacf303c7a9f54b2ba30408d53646a7c6%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636474599462421928&sdata=bvcDWlIJ%2F%2FWQG2axKeeqU6VDgG0PF0RJB3Nf990AKwg%3D&reserved=0>
wwwmpa.mpa-garching.mpg.de<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwwwmpa.mpa-garching.mpg.de&data=02%7C01%7Ccrs07%40mail.aub.edu%7Cacf303c7a9f54b2ba30408d53646a7c6%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636474599462421928&sdata=jV7E2%2Fl6G9uWe1qXIlctliX0nOV7sClb4G1T38CUatg%3D&reserved=0>
From: Yves Revaz <yves.revaz_at_obspm.fr<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fyves.revaz_at_obspm.fr&data=02%7C01%7Ccrs07%40mail.aub.edu%7Cacf303c7a9f54b2ba30408d53646a7c6%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636474599462421928&sdata=RoYqONK2nbHp9ZksEVcdtNOt%2FccOrUl6WMcdipjIW1Q%3D&reserved=0>> Date: Sun, 23 Sep 2007 21:46:58 +0200 Here are my notes concerning the installation of fftw for Gadget-2 :


i configured fftw3 with --enable-typre-prefix, but it says

configure: WARNING: unrecognized options: --enable-type-prefix

i uncommented
OPT += -DNOTYPEPREFIX_FFTW


but i am still getting

pm_periodic.c:16:30: fatal error: rfftw_mpi.h: No such file or directory
 #include <rfftw_mpi.h>
                              ^
compilation terminated.

when compiling gadget2.


thank you for your time

________________________________
From: Jared Coughlin <Jared.W.Coughlin.29_at_nd.edu<mailto:Jared.W.Coughlin.29_at_nd.edu>>
Sent: Monday, November 20, 2017 10:34:33 PM
To: Gadget General Discussion

Subject: Re: [gadget-list] error compiling gadget
Hello! That error means that you have to compile fftw with the type prefixes on and choose the correct type (floating point or double) in the Makefile .
http://www.fftw.org/fftw2_doc/fftw_6.html<https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.fftw.org%2Ffftw2_doc%2Ffftw_6.html&data=02%7C01%7Ccrs07%40mail.aub.edu%7C9754aba657074cefbbb408d530567fe3%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636468070480979364&sdata=imPuBJNTwG8oKvPSB3NnO4ip07IHK%2BTw%2BydOxJTLb8o%3D&reserved=0>

Hope that helps!
-Jared

On Mon, Nov 20, 2017 at 3:26 PM, Yves Revaz <yves.revaz_at_epfl.ch<mailto:yves.revaz_at_epfl.ch>> wrote:
On 20/11/17 21:18, Cynthia Saad (Student) wrote:

right, i was just reading this. i added

OPT += -DH5_USE_16_API
to the makefile.

then make gives me this



pm_periodic.c:21:28: fatal error: srfftw_mpi.h: No such file or directory

srfftw_mpi.h missing from the fftw lib.

They are some detailed instructions on how to compile gadget-2 (and fftw) on mac os or linux here:
https://obswww.unige.ch/lastro/conferences/sf2013/handson.cgi<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fobswww.unige.ch%2Flastro%2Fconferences%2Fsf2013%2Fhandson.cgi&data=02%7C01%7Ccrs07%40mail.aub.edu%7C9754aba657074cefbbb408d530567fe3%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636468070480979364&sdata=xnGhHLUNv8Mt7wsCtXnFlF7CMDGzVGkwi%2Bh5YrU7s%2F8%3D&reserved=0>

Cheers,

yves



 #include <srfftw_mpi.h>
                            ^
compilation terminated.
<builtin>: recipe for target 'pm_periodic.o' failed
make: *** [pm_periodic.o] Error 1



excuse my ignorance

________________________________
From: Yves Revaz <yves.revaz_at_epfl.ch><mailto:yves.revaz_at_epfl.ch>
Sent: Monday, November 20, 2017 10:14:01 PM
To: gadget-list_at_MPA-Garching.MPG.DE<mailto:gadget-list_at_MPA-Garching.MPG.DE>
Subject: Re: [gadget-list] error compiling gadget


Dear Cynthia,

It seems that you are linking with the wrong version of HDF5.
See

https://wwwmpa.mpa-garching.mpg.de/gadget/gadget-list/0432.html<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwwwmpa.mpa-garching.mpg.de%2Fgadget%2Fgadget-list%2F0432.html&data=02%7C01%7Ccrs07%40mail.aub.edu%7C853708b765564ae8bc4108d530539995%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636468057989353575&sdata=9CKxsQq3YqQ7eOomN5XmhiIUFGCsuFSRCZLz4UmU%2BP0%3D&reserved=0>

for more informations.


Cheers,

yves

On 20/11/17 21:09, Cynthia Saad (Student) wrote:

Dear all,

I am new with GADGET and having trouble compiling it. make gives me this error and i can't figure out what to do. https://justpaste.it/1dqg0<https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fjustpaste.it%2F1dqg0&data=02%7C01%7Ccrs07%40mail.aub.edu%7C853708b765564ae8bc4108d530539995%7Cc7ba5b1a41b643e9a1206ff654ada137%7C1%7C0%7C636468057989353575&sdata=VKWpZNkFf8VeoQkaIQzsKcx9ozL645ApM82wDVrCJgY%3D&reserved=0>

what am i doing wrong?

thank you for your much appreciated help,

cynthia


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Received on 2017-12-05 11:48:27

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