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Log in Remember Me? HHeellpp RReeggiisstteerr Forum Compliling subrountines with gfortran - Abaqus 6.11-1

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2013-03-07,

08:37

 

#1

ttiimmddooddwweellll

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CCoommpplliilliinngg ssuubbrroouunnttiinneess wwiitthh ggffoorrttrraann -- AAbbaaqquuss 66 1111--11

 
 

Dear all,

Probably a common problem, but cant find an existing thread with the solution.

 

I am running Abaqus 6.11-1 on Ubuntu 12.04, I was hoping to run the to use 'gfortran' to compile my user subroutines. I have updated the files"abaqus_v6.env" so that

 

Code:

fortCompiler = "gfortran" cppCompiler = "gcc"

 

however when i run a test case I get the following errors in the log file, any help would be great

 

Code:

Abaqus JOB uvarmUel Abaqus 6.11-1

 

Begin Compiling Abaqus/Standard User Subroutines

Thu Mar

7 14:22:39 2013

gfortran: error: unrecognized option '-auto' gfortran: error: unrecognized option '-w90' gfortran: error: unrecognized option '-w95' Abaqus Error: Problem during compilation - uvarmUel.f Abaqus/Analysis exited with errors

Many Thanks

 

Tim

 
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2013-03-17,

14:23

#2

JJoorrggeenn AAddmmiinniissttrraattoorr You may also need to change the actual compilation commands (and it is
JJoorrggeenn
AAddmmiinniissttrraattoorr
You may also need to change the actual compilation commands (and it is platform
dependent).
don't recall writing a summary on using GNU compilers simply because it was hard to
get the linking to work right, and I did not have the time to figure it out.
I
have been told, however, that the upcoming Abaqus version 6.13, should make it
easier to use the GNU compilers.
I
I
may give it a try again once Abaqus 6.13 is released.
-Jorgen
Jorgen Bergstrom, Ph.D.
PolymerFEM Administrator
RReeppllyy WWiitthh QQuuoottee
2013-03-18,
04:24
#3
Join Date:
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After a bit of a battle I have managed to get it working for Abaqus 6.11-1 on Ubuntu
12.04
Hopefully this might save a few people the pain!
As well as updating compiler names (fortCompiler, cppCompiler) in "abaqus_v6.env"
file you have to supress some of the compiler flags. Below is my "abaqus_v6.env" files,
I
have commented out the original code and directly underneath added the new bits in.
Dont just simply copy the file directly, otherwise your license information will be
wrong. Note that in total there are 4 changes.
#
#
System-Wide Abaqus Environment File
-------------------------------------
standard_parallel = ALL
mp_mode = MPI
mp_file_system = (DETECT,DETECT)
#
mp_environment_export = ('MPI_PROPAGATE_TSTP',
'ABA_CM_BUFFERING',
'ABA_CM_BUFFERING_LIMIT',
'ABA_ITERATIVE_SOLVER_VERBOSE',
'ABA_DMPSOLVER_BWDPARALLELOFF',
'ABA_ELP_SURFACE_SPLIT',
'ABA_ELP_SUSPEND',
'ABA_HOME',
'ABA_MEMORY_MODE',
'ABA_MPI_MESSAGE_TRACKING',
'ABA_MPI_VERBOSE_LEVEL',
'ABA_PATH',
'ABA_RESOURCE_MONITOR',
'ABA_RESOURCE_USEMALLINFO',
'ABAQUS_LANG',
'ABAQUSLM_LICENSE_FILE',
'ABQ_CRTMALLOC',
'ABQ_DATACHECK',
'ABQ_RECOVER',
'ABQ_RESTART',
'ABQ_SPLITFILE',
'ABQ_XPL_WINDOWDUMP',
'ABQ_XPL_PARTITIONSIZE',
'ABQLMHANGLIMIT',
'ABQLMQUEUE',
'ABQLMUSER',
'CCI_RENDEZVOUS',
'DOMAIN',
'DOMAIN_CPUS',
'DOUBLE_PRECISION',
'FLEXLM_DIAGNOSTICS',

'FOR0006',

'FOR0064',

'LD_PRELOAD',

'MP_NUMBER_OF_THREADS',

'MPC_GANG',

'MPI_RDMA_NENVELOPE',

'MPI_SOCKBUFSIZE',

'MPI_WORKDIR',

'MPCCI_SERVER',

'MPCCI_INITIAL_EXCHANGE',

'_MPCCI_CCM_CODE_IDS',

'_MPCCI_CODE_IDSTRING',

'ABAQUS_CCI_DEBUG',

 

'NCPUS',

'OMP_DYNAMIC',

'OMP_NUM_THREADS',

 

'OUTDIR',

'PAIDUP',

'PARALLEL_METHOD',

'RAIDEV_NDREG_LAZYMEM',

'ABA_SYMBOLIC_GENERALCOLLAPSE',

'ABA_SYMBOLIC_GENERAL_MAXCLIQUERANK',

'ABA_ADM_MINIMUMINCREASE',

'ABA_ADM_MINIMUMDECREASE',

'IPATH_NO_CPUAFFINITY',

'MALLOC_MMAP_THRESHOLD_',)

import driverUtils, os

#

#

Linux (Opteron/EM64T) Settings:

#

#

Compile and Link command for user subroutines.

#

Compile_cpp and link_exe for Abaqus make utility.

#

import os, re, glob, driverUtils

#

Always use the newest version

fortDefPath = '/' ccDefPath = '/'

## 1) UNCOMMENT THIS TO MAKE ABAQUS WORK WITH GFORTRAN:

#dirLst = glob.glob('/opt/intel/fce/10.1*') #if dirLst:

# dirLst.sort()

# fortDefPath = dirLst[-1] + '/bin'

#dirLst = glob.glob('/opt/intel/cce/10.1*') #if dirLst:

# dirLst.sort()

# ccDefPath = dirLst[-1] + '/bin'

## REPLACE WITH

dirLst = glob.glob('/usr/bin*') if dirLst:

dirLst.sort() fortDefPath = dirLst[-1] + '/bin'

dirLst = glob.glob('/usr/bin') if dirLst:

dirLst.sort() ccDefPath = dirLst[-1] + '/bin'

## CHANGE COMPILER NAMES

# fortCompiler = "ifort"

# cppCompiler = "icpc"

fortCompiler = "gfortran" cppCompiler = "gcc"

if os.path.exists(os.path.join(fortDefPath, fortCompiler)):

fortCmd = os.path.join(fortDefPath, fortCompiler) else:

fortCmd = fortCompiler

if os.path.exists(os.path.join(ccDefPath, cppCompiler)):

cppCmd = os.path.join(ccDefPath, cppCompiler) else:

cppCmd = cppCompiler

#

Avoid signal trapping by the Fortran RTE

os.environ["FOR_IGNORE_EXCEPTIONS"] = "T"

#

Disable messages from the Fotran RTE

os.environ["FOR_DISABLE_DIAGNOSTIC_DISPLAY"] = "T"

#

Turn off use of ACML on AMD processors.

os.environ["ABQ_USE_ACML"] = "0"

#

Do not let QLogic InfiniPath driver set processor affinity.

os.environ["IPATH_NO_CPUAFFINITY"] = "1"

# Add the flag "-free" to the compile_fortran command below to use free-

# format FORTRAN 90 syntax.

## 3) DELETE THE COMPILER FLAGS THAT GFORTRAN DOES NOT UNDERSTAND

#

#

compile_fortran = (fortCmd + " -c -fPIC -auto -mP2OPT_hpo_vec_divbyzero=F

-extend_source -w90 -w95 " +

#

"-WB -I%I")

## AND REPLACE WITH compile_fortran = (fortCmd + " -c -fPIC -I%I")

compile_cpp = (cppCmd +

"

-c -cxxlib -Kc++eh -fPIC " +

"-Krtti -Kc++ -pc64 -restrict -DABQ_LINUX -DABQ_LNX86_64 " + "-DFOR_TRAIL -DHAS_BOOL -DASSERT_ENABLED -D_BSD_TYPES " + "-D_BSD_SOURCE -D_GNU_SOURCE -D_POSIX_SOURCE " + "-D_XOPEN_SOURCE_EXTENDED -D_XOPEN_SOURCE -DHAVE_OPENGL " + "-DHKS_OPEN_GL -DTYPENAME=typename -DGL_GLEXT_PROTOTYPES " + "-D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -we1011 -we120 " + "-we117 -we556 -we144 -we268 -we1224 -we167 -we880 -O0 -I%I" )

#

4) UNCOMMENT THIS:

#link_sl = (fortCmd +

# " -cxxlib -fPIC -threads -shared " +

# "%E -Wl,-soname,%U -o %U %F %A %L %B -parallel -Wl,-Bdynamic " +

# "-i-dynamic -lifport -lifcoremt")

# FOR ABAQUS 6.10 AND HIGHER REPLACE BY:

link_sl = (fortCmd +

"

-gcc-version=%i -fPIC -shared " +

"%E -Wl,-soname,%U -o %U %F %A %L %B -Wl,-Bdynamic " +

"-i-dynamic -lifport -lifcoremt")

#

UNTIL ABAQUS 6.9 REPLACE BY:

#link_sl = (fortCmd +

# " -gcc-version=%i -fPIC -shared " %verId +

# "%E -Wl,-soname,%U -o %U %F %A %L %B -Wl,-Bdynamic " +

# "-i-dynamic -lifport -lifcoremt")

link_exe = (cppCmd + " -cxxlib -fPIC " + "-Wl,-Bdynamic -i-dynamic -o %J %F %M %L %B %O -lpthread")

mp_mpi_implementation = HP hpmpipath = driverUtils.locateFile(os.environ.get('ABA_PATH', ''), 'External/mpi /hpmpi-2.3/bin', 'mpirun') mp_mpirun_path = {HP: hpmpipath} mp_rsh_command = 'rsh -n -l %U %H %C'

#

Remove the temporary names from the namespace

del cppCmd

del fortCmd

del ccDefPath

del cppCompiler

del fortDefPath

del fortCompiler

del hpmpipath

del dirLst

graphicsEnv = driverUtils.locateFile(os.environ['ABA_PATH'],'site','graphicsConfig','env') if graphicsEnv:

execfile(graphicsEnv)

else:

raise 'Cannot find the graphics configuration environment file (graphicsConfig.env)'

del driverUtils, os, graphicsEnv abaquslm_license_file="****"

doc_root=""

doc_root_type="pdf"

academic=RESEARCH

Last edited by timdodwell; 2013-03-18 at 04:39.

RReeppllyy WWiitthh QQuuoottee

RReeppllyy WWiitthh QQuuoottee

2013-05-03,

04:16

#5

ttiimmddooddwweellll

ttiimmddooddwweellll JJuunniioorr MMeemmbbeerr

JJuunniioorr MMeemmbbeerr

ttiimmddooddwweellll JJuunniioorr MMeemmbbeerr

Not sure why it has done that, as I have said I have only tested it for Ubuntu 12.04 and Abaqus 6.11-1

However at a guess, what happens when you delete the flag for 'i-dynamic', i.e in the fourth line of the following bit of code below

# FOR ABAQUS 6.10 AND HIGHER REPLACE BY:

link_sl = (fortCmd +

"

"%E -Wl,-soname,%U -o %U %F %A %L %B -Wl,-Bdynamic " +

"-i-dynamic -lifport -lifcoremt")

-gcc-version=%i -fPIC -shared " +

Originally Posted by eekkmmoooo Hi Timdodwell, Thank you very much for your detailed instruction on
Originally Posted by eekkmmoooo
Hi Timdodwell,
Thank you very much for your detailed instruction on how to link gfortran to abaqus.
However, when I followed your steps and change the abqus_v6.env file, I got the
following error while running a user-subroutine.
"gfortran: error: unregconized command line option '-i-dynamic'"
Is there any chance you might know the problem? I am using Ubuntu 12.10, abaqus
6.12-2.
Any help is much appreciated. Thank you in advance.
RReeppllyy WWiitthh QQuuoottee

RReeppllyy WWiitthh QQuuoottee

2013-07-24,

05:16

#7

ccaalleeddoonniiaa

ccaalleeddoonniiaa JJuunniioorr MMeemmbbeerr

JJuunniioorr MMeemmbbeerr

ccaalleeddoonniiaa JJuunniioorr MMeemmbbeerr

LLiinnkkiinngg GGFFoorrttrraann ttoo AAbbaaqquuss

Hello everybody,

am trying to link gfortran to Abaqus 6.12-1 using the instructions above. It does not work for me.

I

Step 1 (compiling) works. I changed:

-

compile_fortran=['ifort', '/c','/DABQ_WIN86_64',

'/iface:cref', '/recursive', '/Qauto-scalar', '/QxW', '/nologo', '/heap-arrays:1', '/Od', '/include:%I']

-

 

to:

-

compile_fortran = ('gfortran' + " -c ")

-

Step 2 (linking) does not work. I changed:

-

link_sl=['LINK', '/nologo', '/INCREMENTAL:NO', '/subsystem:console', '/machine:AMD64', '/NODEFAULTLIB:LIBC.LIB', '/NODEFAULTLIB:LIBCMT.LIB', '/DEFAULTLIB:OLDNAMES.LIB', '/DEFAULTLIB:LIBIFCOREMD.LIB', '/DEFAULTLIB:LIBIFPORTMD', '/DEFAULTLIB:LIBMMD.LIB', '/DEFAULTLIB:MSVCRT.LIB', '/DEFAULTLIB:kernel32.lib', '/DEFAULTLIB:user32.lib',

'/DEFAULTLIB:advapi32.lib',

'/FIXED:NO', '/dll', '/def:%E', '/out:%U', '%F', '%A', '%L', '%B', 'oldnames.lib', 'user32.lib', 'ws2_32.lib', 'netapi32.lib', 'advapi32.lib']

-

 

to:

-

link_sl = ('gfortran' +

"

-gcc-version=%i -fPIC -shared " +

"%E -Wl,-soname,%U -o %U %F %A %L %B -Wl,-Bdynamic " + "-i-dynamic -lifport -lifcoremt")

-

resulting ERRORs:

-

Begin Compiling Abaqus/Standard User Subroutines

24.07.2013

11:41:31

End Compiling Abaqus/Standard User Subroutines

24.07.2013

11:41:31

Begin Linking Abaqus/Standard User Subroutines

24.07.2013

11:41:31

gfortran: error: uamp_daempfergeschwindigkeit.obj: No such file or directory

gfortran: error: /LIBPATH:C:\Abaqus\Abaqus6.12-1\6.12-1\code\lib: Invalid argument gfortran: error: /LIBPATH:C:\Abaqus\Abaqus6.12-1\6.12-1\code\bin\SMAExternal:

Invalid argument gfortran: error: standardB.lib: No such file or directory gfortran: error: ABQSMABasCoreUtils.lib: No such file or directory gfortran: error: ABQSMAAbuLicense.lib: No such file or directory gfortran: error: unrecognized command line option '-i-dynamic' Abaqus Error: Problem during linking - Abaqus/Standard User Subroutines. This error may be due to a mismatch in the Abaqus user subroutine arguments. These arguments sometimes change from release to release, so user subroutines used with a previous release of Abaqus may need to be adjusted. Abaqus/Analysis exited with errors

-

when I remove '-i-dynamic' and changed it to:

-

link_sl = ('gfortran' +

"

-gcc-version=%i -fPIC -shared " +

"%E -Wl,-soname,%U -o %U %F %A %L %B -Wl,-Bdynamic " +

"

-lifport -lifcoremt")

-

resulting ERRORs:

-

Begin Compiling Abaqus/Standard User Subroutines

24.07.2013

11:44:35

End Compiling Abaqus/Standard User Subroutines

24.07.2013

11:44:35

Begin Linking Abaqus/Standard User Subroutines

24.07.2013 11:44:35 gfortran: error: uamp_daempfergeschwindigkeit.obj: No such file or directory gfortran: error:

24.07.2013 11:44:35 gfortran: error: uamp_daempfergeschwindigkeit.obj: No such file or directory gfortran: error: /LIBPATH:C:\Abaqus\Abaqus6.12-1\6.12-1\code\lib: Invalid argument gfortran: error: /LIBPATH:C:\Abaqus\Abaqus6.12-1\6.12-1\code\bin\SMAExternal:

Invalid argument gfortran: error: standardB.lib: No such file or directory gfortran: error: ABQSMABasCoreUtils.lib: No such file or directory gfortran: error: ABQSMAAbuLicense.lib: No such file or directory

-

For information: uamp_daempfergeschwindigkeit.for is the name of my subroutine.

Can someone help me and explain where the problem is, please?

Best wishes

Clarissa

RReeppllyy WWiitthh QQuuootteewhere the problem is, please? Best wishes Clarissa 2013-11-18, 12:27 #8   Join Date: 2013-05

2013-11-18,

12:27

#8

 

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Hi Clarissa, May I know what is the operating system you are using? It may be important Eng Kuan

 
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