Installing garfield to Ubuntu 10.04 Lucid Lynx - gfortran

[Cenko]

After struggling for a while, I managed to install garfield (With important help of dinofelis) and decided to share my experince on compiling garfield on Ubuntu 10.04.

For information of garfield: http://garfield.web.cern.ch/garfield/

If you don't have it yet, install gfortran

sudo apt-get install gfortran

install cernlib,libgsl from repositories

sudo apt-get install cernlib libgsl0-dev nypatchy

Create a directory (lets say /home/username/garfield/) and copy all necessary files from website to this directory:

garfield-7.car
garfadd-9.cra
garfield-9.cra
garfield.hlp
heed101garf.car
magboltz-7.car
patchy_step (It is defined as "Script to run Patchy" in the website)

(If you want another version of garfield you should download the corresponding .cra files.

Get NeBem from either its website, or the afs folders:

/afs/cern.ch/user/r/rjd/Garfield/Files/neBEM/V1.7e

For ease, copy this folder directly to your working folder as

./neBEM/V1.7e/

Now the essential thing: Normaly program is written to be compiled in g77, when you use gfortran, you get an error like:

undefined reference to `iargc_'

In gfortran, instead of iargc_() there is _gfortran_iargc() function. So you need to make your compiler
recognize iargc_() as _gfortran_iargc(). To do this paste this little code into a file named

gfortran_iargc.c

and save it somewhere in your working directory, for example: ./extras/iarg.d/gfortran_iargc.c

extern int _gfortran_iargc(void);
int iargc_()
{
return _gfortran_iargc();
}

go to this directory and compile the code as:

gfortran -c _gfortran_iargc.c

It will create the file "_gfortran_iargc.o". Note that in the makefile you'll need to set variable $DUMMYIARGCOBJ
to the location of this file.(see: makefile)

Now you are ready to compile garfield, you can use a sample makefile and modify your folder names. To compile simply write

make garfield-9

The sample makefile is attached. YOu should change the name to makefile after downloading

[flueke]

First of all, thanks for your post! The Makefile and especially the gfortran_iargc part are very helpful.

I'm currently trying to build garfield-9 on a 32-bit Ubuntu 10.10 system. All the fortran files compile fine but at the final linking stage I run into this error:

gfortran  -o ~/garfield/garfield-9/bin/garfield-9 *.o ~/garfield/garfield-9/extras/gfortran_iargc.o \
        ./neBEM/V1.7.2/obj/GarfieldInterface.o ./neBEM/V1.7.2/obj/neBEMInterface.o \
        ./neBEM/V1.7.2/obj/ReTriM.o ./neBEM/V1.7.2/obj/ComputeProperties.o \
        ./neBEM/V1.7.2/obj/neBEM.o \
        -Wl,-static -lgraflib -lgrafX11 -lmathlib -Wl,-dy -lX11 -lkernlib -llapack -lm -lpacklib -lnsl -lcrypt -ldl -lgfortran -std=c99 \
        -Iinclude -L./neBEM/V1.7.2/lib \
        -lNR -lVector -lIsles  -L/usr/local/lib -lgslcblas -lgsl -lm -lgfortran
celcal.o: In function `celcal_':
celcal.f:(.text+0x17f5): undefined reference to `bemvoq_'
celspr.o: In function `celspr_':
celspr.f:(.text+0x1307): undefined reference to `bemvoq_'
celspr.f:(.text+0x2177): undefined reference to `bemvoq_'
celspr.f:(.text+0x2df6): undefined reference to `bemvoq_'
celspr.f:(.text+0x365e): undefined reference to `bemvoq_'
celspr.o:celspr.f:(.text+0x427e): more undefined references to `bemvoq_' follow
collect2: ld returned 1 exit status
make: *** [garfield-9] Error 1

I'm not sure whether `bemvoq_` should be part of libneBEM or if the definition is just missing from garfield-7.car. Note: I was only able to get versions 1.7.1 and 1.7.2 of neBEM, not version 1.7e which you used to build garfield.

Any help or suggestions would be much appreciated.

[igal]

To install garfield on Ubuntu 10.04 LTS - the Lucid Lynx for a 64 bit machine some minor modifications have to be applied to Cenk's installation method

1/ install all lib32 via synaptic or sudo apt-get install ia32-libs

2/ some other libraries have to be added (I copied it from my 32bit desktop which is also working with Lucid Lynx)

libgraflib.a
libgraflib.so.1_gfortran.2006
libgraflib.so.1_gfortran
libgraflib.so
libkernlib.a
libkernlib.so.1_gfortran.2006
libkernlib.so.1_gfortran
libkernlib.so
libmathlib.a
libmathlib.so.2_gfortran.2006
libmathlib.so.2_gfortran
libmathlib.so
libpacklib1-gfortran
libpacklib.so.1_gfortran.2006
libpacklib.so.1_gfortran -> libpacklib.so.1_gfortran.2006
libpacklib.so -> libpacklib.so.1_gfortran.2006
libpacklib-lesstif.so.1_gfortran.2006
libpacklib-lesstif.so.1_gfortran -> libpacklib-lesstif.so.1_gfortran.2006
libpacklib-lesstif.so -> libpacklib-lesstif.so.1_gfortran.2006
libpacklib-lesstif.a
libpacklib.a
libgrafX11.a
libgrafX11.so.1_gfortran.2006
libgrafX11.so.1_gfortran
libgrafX11.so
liblapack.a
liblapackgf-3.a
liblapackgf-3.so
liblapack.so
liblapack.so.3gf.0
liblapack.so.3gf
libblas.so.3gf.0
libblas.so.3gf

3/
gfortran -c _gfortran_iargc.c becomes gfortran -m32 -c _gfortran_iargc.c

[igal]

4/ compile neBEM with -m32 flag

G77=gfortran -m32 # on more recent versions of linux

CFLAGS=-Wall -std=c99 -O3 -m32 # last option necessary for Garfield

5/ in neBEM/V1.7e/lib
cp libIsles32.a libIsles.a

6/ compile garfield with -m32 flag and forcing to read the lib32 by -L/usr/lib32

FC = gfortran -m32
#LF=-Wl,-static -lgraflib -lgrafX11 -lmathlib -Wl,-dy -lX11 -lkernlib -llapack -lm \
#-lpacklib -lnsl -lcrypt -ldl -lgfortran
LF=-Wl,-static -L/usr/lib32 -lgraflib -lgrafX11 -lmathlib -Wl,-dy -lX11 -lkernlib -llapack -lm \
-lpacklib -lnsl -lcrypt -ldl -lgfortran

[psyentist88]

I am trying to install Garfield on a 64 bit Ubuntu 10.10 recently, but so far without any succes.

Following Cenko's and igal's advices, I get this:

gfortran -m32  -o ~/garfield/bin//garfield-9 *.o ~/garfield//extras/iarg.d/gfortran_iargc.o \
    ./neBEM/V1.7.2/obj/GarfieldInterface.o ./neBEM/V1.7.2/obj/neBEMInterface.o \
    ./neBEM/V1.7.2/obj/ReTriM.o ./neBEM/V1.7.2/obj/ComputeProperties.o \
    ./neBEM/V1.7.2/obj/neBEM.o \
    -Wl,-static -L/usr/lib32 -lgraflib -lgrafX11 -lmathlib -Wl, -dy -lX11 -lkernlib -llapack -lm -lpacklib -lnsl -lcrypt -ldl -lgfortran -std=c99 \
    -Iinclude -L./neBEM/V1.7.2/lib \
    -lNR -lVector -lIsles  -L/usr/local/lib -lgslcblas -lgsl -lm -lgfortran
/usr/bin/ld: cannot find : No such file or directory
/usr/lib32/libX11.a(CrGlCur.o): In function `open_library':
(.text+0x3b): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/bin/ld: cannot find -lgcc_s
/usr/lib/gcc/x86_64-linux-gnu/4.4.5/32/libgfortran.a(getlog.o): In function `_gfortran_getlog':
(.text+0x32): warning: Using 'getpwuid' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/lib32/libX11.a(xim_trans.o): In function `_XimXTransSocketUNIXConnect':
(.text+0xe23): warning: Using 'getaddrinfo' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking
/usr/bin/ld: cannot find -lgcc_s
collect2: ld returned 1 exit status
make: *** [garfield-9] Error 1

By the way /usr/bin/ld exists. Does anyone have a clue what is wrong?

BTW I have put a 32 bit Ubuntu 10.10 on VirtualBox just in order to install Garfield. With the above mentioned method, it works for me too.

[h010410225]

thanks for the post, i have a problem here,
huang_sun@huang:~/garfield$ make garfield-9
rm *.f *.o
rm: 无法删除"*.f": 没有那个文件或目录 (can't delete '*.f',no such file or dir)
rm: 无法删除"*.o": 没有那个文件或目录
make: [garfield-9.f] 错误 1 (忽略) (err 1, ignor)
./patchy_step garfield-9

Nypatchy executing with files / options
.........
73 + +USE,P=SIGNAL,D=SIGADM,T=I.
74 + +USE,P=SIGNAL,D=SIGFLS,T=I.
75 + +USE,P=SIGNAL,D=SIGWRT,T=I.

76 + +PAM,LUN=11,T=a,C. garfield-7.car

***!!! OPEN fails for file: garfield-7.car
Perror has: Illegal seek

***!!! Kill the run for: OPEN failure !!!***
: not foundep: 3:
make: *** [garfield-9.f] 错误 127 (err 127)
,

could anyeone give me some help

[yankang]

Thanks to you all. The discussion is very helpful. But i have a problem. Just like h010410225:

[yanqiang@localhost garfield]$ make garfield-9
rm *.f *.o
rm: cannot remove `*.f': No such file or directory
rm: cannot remove `*.o': No such file or directory
make: [garfield-9.f] Error 1 (ignored)
./patchy_step garfield-9
./patchy_step: line 1: nypatchy: command not found
make: *** [garfield-9.f] Error 127

what this message means? I have checked the content of patchy_step, it only have two lines: nypatchy - $1 $1 - - - - - - - - - :GO
# less y.lis
What the command nypatchy means?
Any help will be most welcomed!!

[Cenko]

What the command nypatchy means?
Any help will be most welcomed!!

Sorry for not including that, it is part of CERNLIB, that you can download from ubuntu repositories.I'm adding it to main post. You can simply install it as follows before compiling garfield:

sudo apt-get install nypatchy

[yankang]

Thank you very much, Cenko! This problem has been solved by using your method. And another command fcaplit could be solved in the same way. Thank you !! Best wishes!!

[yankang]

Dear all, thank you for your post！After some problems were solved, more problems occured. Now a problem I encountered is about libpacklib.a. When the gfortran tried to link the program, an error appeared like this:

........
dzbkhd.F:(.text+0x1fb): undefined reference to `do_fio'
/home/yanqiang/cern/2006/lib/libpacklib.a(dzbkhd.o):dzbkhd.F:(.text+0x24d): more undefined references to `do_fio' follow
/home/yanqiang/cern/2006/lib/libpacklib.a(dzbkhd.o): In function `dzbkhd_':
dzbkhd.F:(.text+0x3e6): undefined reference to `e_wsfi'
dzbkhd.F:(.text+0x429): undefined reference to `s_copy'
/home/yanqiang/cern/2006/lib/libpacklib.a(dziopr.o): In function `dziopr_':
dziopr.F:(.text+0x1a): undefined reference to `s_copy'
dziopr.F:(.text+0x2d): undefined reference to `s_copy'
dziopr.F:(.text+0xa7): undefined reference to `s_wsfi'
dziopr.F:(.text+0xbb): undefined reference to `do_fio'
dziopr.F:(.text+0xcf): undefined reference to `do_fio'
dziopr.F:(.text+0xe3): undefined reference to `do_fio'
dziopr.F:(.text+0x105): undefined reference to `do_fio'
dziopr.F:(.text+0x10a): undefined reference to `e_wsfi'
dziopr.F:(.text+0x164): undefined reference to `s_copy'
/home/yanqiang/cern/2006/lib/libpacklib.a(fzialn.o): In function `fzialn_':
fzialn.F:(.text+0x6a): undefined reference to `s_rsfe'
fzialn.F:(.text+0x8e): undefined reference to `do_fio'
fzialn.F:(.text+0xa3): undefined reference to `e_rsfe'
fzialn.F:(.text+0x1db): undefined reference to `s_rsfe'
fzialn.F:(.text+0x1fb): undefined reference to `do_fio'
fzialn.F:(.text+0x20c): undefined reference to `e_rsfe'
/home/yanqiang/cern/2006/lib/libpacklib.a(fzoaln.o): In function `fzoaln_':
fzoaln.F:(.text+0x81): undefined reference to `s_wsfe'
fzoaln.F:(.text+0xa1): undefined reference to `do_fio'
fzoaln.F:(.text+0xb2): undefined reference to `e_wsfe'
/home/yanqiang/cern/2006/lib/libpacklib.a(uh1toc.o): In function `uh1toc_':
uh1toc.F:(.text+0x49): undefined reference to `s_copy'
/home/yanqiang/cern/2006/lib/libpacklib.a(dziopd.o): In function `dziopd_':
dziopd.F:(.text+0x1b): undefined reference to `s_copy'
dziopd.F:(.text+0x2e): undefined reference to `s_copy'
dziopd.F:(.text+0xa4): undefined reference to `s_copy'
dziopd.F:(.text+0xe5): undefined reference to `s_copy'
/home/yanqiang/cern/2006/lib/libpacklib.a(dziopd.o):dziopd.F:(.text+0xfb): more undefined references to `s_copy' follow
/home/yanqiang/cern/2006/lib/libpacklib.a(dziopd.o): In function `dziopd_':
dziopd.F:(.text+0x288): undefined reference to `s_wsfi'
dziopd.F:(.text+0x29c): undefined reference to `do_fio'
dziopd.F:(.text+0x2c0): undefined reference to `do_fio'
dziopd.F:(.text+0x2d4): undefined reference to `do_fio'
dziopd.F:(.text+0x2d9): undefined reference to `e_wsfi'
dziopd.F:(.text+0x3cd): undefined reference to `s_copy'
dziopd.F:(.text+0x50e): undefined reference to `s_wsfi'
dziopd.F:(.text+0x52b): undefined reference to `do_fio'
dziopd.F:(.text+0x53f): undefined reference to `do_fio'
dziopd.F:(.text+0x544): undefined reference to `e_wsfi'
dziopd.F:(.text+0x596): undefined reference to `s_wsfi'
dziopd.F:(.text+0x5f0): undefined reference to `s_wsfi'
dziopd.F:(.text+0x64b): undefined reference to `s_wsfi'
dziopd.F:(.text+0x6b0): undefined reference to `s_wsfi'
dziopd.F:(.text+0x6c4): undefined reference to `do_fio'
dziopd.F:(.text+0x6c9): undefined reference to `e_wsfi'
dziopd.F:(.text+0x702): undefined reference to `s_wsfi'
........
collect2: ld returned 1 exit status
make: *** [garfield-9] Error 1

Nearly every *.o file of libpacklib.a has this kind of error. I have tried the cernlibs of version 2003 , following the guide from http://www.icepp.s.u-tokyo.ac.jp/~nanjyo /html/garfield.html, and the cernlibs of version 2006 compiled from the source, but all effort failed.I don't know where the problem lies, the cernlib(libpacklib.a) or other place?

The make file I used was modified from what provided by Cenko, and I post it as attachment. Could anyone help me?