From bentivegna at cct.lsu.edu  Tue Dec  1 17:16:46 2009
From: bentivegna at cct.lsu.edu (Eloisa Bentivegna)
Date: Tue, 01 Dec 2009 17:16:46 -0600
Subject: [Users] Flag in GetCactus script.
Message-ID: <4B15A3DE.7070706@cct.lsu.edu>

Hi,

the current version of the GetCactus script has the following logic for 
the flag -updateflesh:


         if ($defaults)
         {
            if (defined $updateflesh) {
               print " yes\n";
               $updatetheflesh = 1;
            } else {
               print " no\n";
            }
         }
         else
         {
            $answer = <STDIN>;
         }

which makes it ignore said flag unless -defaults is also given. Is this 
the intended behavior?

Thanks,
Eloisa

From schnetter at cct.lsu.edu  Wed Dec  2 12:38:21 2009
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Wed, 2 Dec 2009 12:38:21 -0600
Subject: [Users] Fwd:  Fwd: Linking Error with Fortran routines
In-Reply-To: <E17ECD7F-6E6C-4F79-80DF-40FEE99FACA4@gmail.com>
References: <17D0C4B4-30E6-46DC-81F7-96E4DBE59464@gmail.com>
	<E17ECD7F-6E6C-4F79-80DF-40FEE99FACA4@gmail.com>
Message-ID: <1BFF2E60-025E-4D68-9D8B-BAF2A470CDA9@cct.lsu.edu>

Fahad

This looks as if Cactus does not auto-detect which Fortran run-time library is necessary.  Since Cactus combines C, C++, and Fortran, you will have to select this manually.

Which machine are you using?  Which operating system is this?

It is likely that the missing option looks similar to

	LDFLAGS = -lgfortran

but you may also need to set other linker options, and/or may need to specify the directory where this library is located.

The Cactus web site has working configurations for a number of machines that we commonly use.  You could have a look there for inspiration.

-erik

On Nov 29, 2009, at 10:02 , Fahad Nasir wrote:

> Begin forwarded message:
> 
>> From: Fahad Nasir <fahadpro at gmail.com>
>> Date: November 29, 2009 5:02:19 PM GMT+01:00
>> To: Erik Schnetter <schnetter at cct.lsu.edu>
>> Subject: Re: [Users] Fwd: Linking Error with Fortran routines
>> 
>> Still encountering problems when try to compile AEIThrons/BSSN_MoL even with gfortran and gcc.
>> 
>> Creating cactus_gf in /Users/fahadnasir/cactus/exe from CactusEinstein/ADMBase CactusEinstein/ADMCoupling CactusEinstein/ADMMacros AEIThorns/BSSN_MoL CactusBase/Boundary CactusBase/CartGrid3D CactusBase/CoordBase CactusEinstein/CoordGauge CactusBase/IOUtil CactusBase/MoL CactusPUGH/PUGH CactusEinstein/SpaceMask CactusEinstein/StaticConformal CactusBase/SymBase CactusBase/Time CactusUtils/TimerReport
>> ld: warning: alignment lost in merging tentative definition _spacemaskrest_
>> ld: warning: alignment lost in merging tentative definition _admmacrosrest_
>> Undefined symbols:
>>  "__gfortran_runtime_error_at", referenced from:
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_lapsesource_ in libthorn_BSSN_MoL.a(LapseSource.F.o)
>>      _adm_bssn_lapsesource_ in libthorn_BSSN_MoL.a(LapseSource.F.o)
>>  "__gfortran_transfer_character", referenced from:
>>      _adm_bssn_setup_ in libthorn_BSSN_MoL.a(PreLoop.F.o)
>>  "__gfortran_st_write", referenced from:
>>      _adm_bssn_setup_ in libthorn_BSSN_MoL.a(PreLoop.F.o)
>>  "__gfortran_st_write_done", referenced from:
>>      _adm_bssn_setup_ in libthorn_BSSN_MoL.a(PreLoop.F.o)
>>  "__gfortran_runtime_error", referenced from:
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_lapsesource_ in libthorn_BSSN_MoL.a(LapseSource.F.o)
>>  "__gfortran_transfer_real", referenced from:
>>      _adm_bssn_setup_ in libthorn_BSSN_MoL.a(PreLoop.F.o)
>>  "__gfortran_os_error", referenced from:
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_sources_ in libthorn_BSSN_MoL.a(Sources.F.o)
>>      _adm_bssn_lapsesource_ in libthorn_BSSN_MoL.a(LapseSource.F.o)
>> ld: symbol(s) not found
>> collect2: ld returned 1 exit status
>> make[1]: *** [/Users/fahadnasir/cactus/exe/cactus_gf] Error 1
>> make: *** [gf] Error 2
>> 
>> 
>> 
>> On Nov 28, 2009, at 9:45 PM, Erik Schnetter wrote:
>> 
>>> On Nov 28, 2009, at 14:10 , Fahad Nasir wrote:
>>> 
>>>>>> Hi,
>>>>>> 
>>>>>> I am using mac osx 1.6.1..snowleopard with xcode 3.2....I have trouble with Fortran routines. All went okay if i use only routines with c++ or c code..I am using Absoft fortran compiler..here is the screen ouput..
>>>>>> 
>>>>>> Preprocessing /Users/fahadnasir/cactus/configs/local/bindings/build/WaveToyF77/cctk_ThornBindings.c
>>>>>> Compiling /Users/fahadnasir/cactus/configs/local/bindings/build/WaveToyF77/cctk_ThornBindings.c
>>>>>> Postprocessing /Users/fahadnasir/cactus/configs/local/bindings/build/WaveToyF77/cctk_ThornBindings.c
>>>>>> ________________________________________________________________________
>>>>>> Creating /Users/fahadnasir/cactus/configs/local/lib/libthorn_WaveToyF77.a
>>>>>> ranlib: archive member: /Users/fahadnasir/cactus/configs/local/lib/libthorn_WaveToyF77.a(cctk_ThornBindings.c.o) cputype (16777223) does not match previous archive members cputype (7) (all members must match)
>>>>>> ranlib: archive library: /Users/fahadnasir/cactus/configs/local/lib/libthorn_WaveToyF77.a will be fat and ar(1) will not be able to operate on it
>>>>>> ar: internal ranlib command failed
>>>>>> make[2]: *** [/Users/fahadnasir/cactus/configs/local/lib/libthorn_WaveToyF77.a] Error 1
>>>>>> make[1]: *** [/Users/fahadnasir/cactus/configs/local/lib/libthorn_WaveToyF77.a] Error 2
>>>>>> make: *** [local] Error 2
>>> 
>>> Farid
>>> 
>>> When you combine compilers from different vendors (gcc and Absoft), then you need to make sure that they are binary compatible.  By default, Xcode 3.2 will produce 64 bit executable, and I don't know what Absoft produces.  I strongly suggest to use a single compiler vendor.  I don't know how old the Xcode version of gcc is; if it is too old, it will not have a Fortran compiler included.  In this case, you can install a recent version of gcc (including g++ and gfortran) yourself.
>>> 
>>> I use MacPorts for this, and I use gcc 4.4.  This works without problems.  Since you will then have multiple compilers installed, you will need to tell Cactus which one to use.  The best way to do that is an options file which sets the CC, CXX, F77, and F90 variables; I hope that the users' guide has a good example for this.
>>> 
>>> -erik
>>> 
>>> -- 
>>> Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/
>>> 
>>> 
>>> 
>> 
> 
> _______________________________________________
> Users mailing list
> Users at cactuscode.org
> http://www.cactuscode.org/mailman/listinfo/users


-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/





From fahadpro at gmail.com  Fri Dec  4 06:54:36 2009
From: fahadpro at gmail.com (fahad nasir)
Date: Fri, 4 Dec 2009 13:54:36 +0100
Subject: [Users] Linking Error with Fortran routines
In-Reply-To: <AC09C7E2-81B9-4723-B791-48A6E3248289@gmail.com>
References: <E5EC4899-B90F-489D-BE96-59C5E5EE6A1A@gmail.com>
	<120CE1DF-64C1-4648-B00B-3A18F49A7141@cct.lsu.edu>
	<AC09C7E2-81B9-4723-B791-48A6E3248289@gmail.com>
Message-ID: <db540a6e0912040454n114f3db8ubf5adbebbb7756f1@mail.gmail.com>

Hi,

Actually i am working on astrophysics project and using CactusEinstein and
AEIThorns arrangments but surprisingly setting     LDFLAGS = -lgfortran
worked like charm.  i am using mac osx 1.5.2 with xcode 3.0 and with
gcc4.4.1 compiler. I was able to compile my relevant thorns . Still i have
question about hdf5. what version have build in stream virtual driver  and
which version will work mac osx 1.5.2..

Thanks..I appologize of the late response....


Hi Farad,

I hope you are making progress with your Cactus installation. What are you
using Cactus for? I see you are compiling our relativity thorns below, are
you working in astrophysics or using Cactus for a different project? If you
aren't trying to run an astrophysics problems we might be able to help you
with a set of thorns more appropriate for what you are looking at that will
be easier to compile.

Best wishes

Gabrielle



On Dec 3, 2009, at 4:05, Allen Gabrielle <gallen at cct.lsu.edu> wrote:


Do you know who this guy is?


On Dec 2, 2009, at 12:38 PM, Erik Schnetter wrote:


Fahad


This looks as if Cactus does not auto-detect which Fortran run-time library
is necessary.  Since Cactus combines C, C++, and Fortran, you will have to
select this manually.


Which machine are you using?  Which operating system is this?


It is likely that the missing option looks similar to


  LDFLAGS = -lgfortran


but you may also need to set other linker options, and/or may need to
specify the directory where this library is located.


The Cactus web site has working configurations for a number of machines that
we commonly use.  You could have a look there for inspiration.

erik..
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From fahadpro at gmail.com  Fri Dec  4 08:02:34 2009
From: fahadpro at gmail.com (fahad Nasir)
Date: Fri, 4 Dec 2009 15:02:34 +0100
Subject: [Users] Linking Error with Fortran routines
In-Reply-To: <db540a6e0912040454n114f3db8ubf5adbebbb7756f1@mail.gmail.com>
References: <E5EC4899-B90F-489D-BE96-59C5E5EE6A1A@gmail.com>
	<120CE1DF-64C1-4648-B00B-3A18F49A7141@cct.lsu.edu>
	<AC09C7E2-81B9-4723-B791-48A6E3248289@gmail.com>
	<db540a6e0912040454n114f3db8ubf5adbebbb7756f1@mail.gmail.com>
Message-ID: <F37C7ABA-0BF5-4AD4-9E8E-DBB180AFB889@gmail.com>

I have tried to configure  hdf5-1.8.4 by ' --enable-stream-vdf '  
option but it seems that hdf5.1.8.4 doest recognize it...any  
ideas...which eventually generate errors while configuring Cactus with  
hdf5....

./configure --prefix=/usr/local/hdf5 --enable-stream-vdf --disable- 
shared
configure: WARNING: unrecognized options: --enable-stream-vdf



On Dec 4, 2009, at 1:54 PM, fahad nasir wrote:

>
> Hi,
>
> Actually i am working on astrophysics project and using  
> CactusEinstein and AEIThorns arrangments but surprisingly  
> setting     LDFLAGS = -lgfortran worked like charm.  i am using mac  
> osx 1.5.2 with xcode 3.0 and with gcc4.4.1 compiler. I was able to  
> compile my relevant thorns . Still i have question about hdf5. what  
> version have build in stream virtual driver  and which version will  
> work mac osx 1.5.2..
>
> Thanks..I appologize of the late response....
>
>
>> 	
>> Hi Farad,
>>
>> I hope you are making progress with your Cactus installation. What  
>> are you using Cactus for? I see you are compiling our relativity  
>> thorns below, are you working in astrophysics or using Cactus for a  
>> different project? If you aren't trying to run an astrophysics  
>> problems we might be able to help you with a set of thorns more  
>> appropriate for what you are looking at that will be easier to  
>> compile.
>>
>> Best wishes
>>
>> Gabrielle
>>
>>
>>>
>>> On Dec 3, 2009, at 4:05, Allen Gabrielle <gallen at cct.lsu.edu> wrote:
>>>
>>>>
>>>> Do you know who this guy is?
>>>>
>>>> On Dec 2, 2009, at 12:38 PM, Erik Schnetter wrote:
>>>>
>>>>> Fahad
>>>>>
>>>>> This looks as if Cactus does not auto-detect which Fortran run- 
>>>>> time library is necessary.  Since Cactus combines C, C++, and  
>>>>> Fortran, you will have to select this manually.
>>>>>
>>>>> Which machine are you using?  Which operating system is this?
>>>>>
>>>>> It is likely that the missing option looks similar to
>>>>>
>>>>>   LDFLAGS = -lgfortran
>>>>>
>>>>> but you may also need to set other linker options, and/or may  
>>>>> need to specify the directory where this library is located.
>>>>>
>>>>> The Cactus web site has working configurations for a number of  
>>>>> machines that we commonly use.  You could have a look there for  
>>>>> inspiration.
>>>>> erik..
>>
>>
>>
>>
>>
>
>

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From knarf at cct.lsu.edu  Mon Dec  7 14:25:29 2009
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Mon, 7 Dec 2009 14:25:29 -0600
Subject: [Users] General EOS interface
Message-ID: <20091207202529.GT9360@numrel07.cct.lsu.edu>

Hi,

as agreed by the authors of the general EOS interface, the development
of the new interface has now been moved to the Cactus server inside the
CactusEOS arrangement. You can get it by adding the following to your
thornlist:

!REPOSITORY_LOCATION cvs.cactuscode.org
!REPOSITORY_NAME /arrangements
!REPOSITORY_USER cvs_anon
CactusEOS/EOSG_Base
CactusEOS/EOSG_Polytrope
CactusEOS/EOSG_IdealFluid
CactusEOS/EOSG_Hybrid

As you can see, we took the opportunity to change the names of the
thorns (for consistency and shortness). The content itself was not
changed for the move, but you should expect some development in the near
future.

By moving these thorns to Cactus, they are now also freely available.
Thanks go to the authors of those thorns (mainly Ian Hawke and Christian
Ott) and to the Whisky developers for hosting the thorns in the past.

Frank

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From knarf at cct.lsu.edu  Wed Dec  9 10:29:27 2009
From: knarf at cct.lsu.edu (Frank Loeffler)
Date: Wed, 9 Dec 2009 10:29:27 -0600
Subject: [Users] Flag in GetCactus script.
In-Reply-To: <4B15A3DE.7070706@cct.lsu.edu>
References: <4B15A3DE.7070706@cct.lsu.edu>
Message-ID: <20091209162927.GY9360@numrel07.cct.lsu.edu>

On Tue, Dec 01, 2009 at 05:16:46PM -0600, Eloisa Bentivegna wrote:
> which makes it ignore said flag unless -defaults is also given. Is this 
> the intended behavior?

I cannot think of a reason why it should be ignored. I changed the
script to respect -updateflesh also without -defaults.

Frank

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From schnetter at cct.lsu.edu  Tue Dec 15 23:15:16 2009
From: schnetter at cct.lsu.edu (Erik Schnetter)
Date: Tue, 15 Dec 2009 23:15:16 -0600
Subject: [Users] Solution: Out of memory on Kraken
Message-ID: <ADCAD1C6-4C5C-4DBA-BCBC-85D2A793EB42@cct.lsu.edu>

I noticed that the SimFactory default options for running jobs on Kraken did not include the "-N" option.  The default settings for Kraken allow only 1.3 GByte per MPI process on Kraken.  This setting is wrong if either fewer than all 12 cores are used, or if OpenMP is used.  In this case, one needs to allow more memory per MPI process, because other some of the nodes' memory will remain unused.

I have just modified the SimFactory job submission script for Kraken to include the necessary -N option.  In one particular case involving OpenMP, this allowed me to reduce the number of nodes by a factor of 4.

If you have problems running Cactus on Kraken and are running out of memory, please try this, and give feedback whether this helps you.

-erik

-- 
Erik Schnetter <schnetter at cct.lsu.edu>   http://www.cct.lsu.edu/~eschnett/





From gallen at cct.lsu.edu  Wed Dec 16 22:41:08 2009
From: gallen at cct.lsu.edu (Allen Gabrielle)
Date: Wed, 16 Dec 2009 23:41:08 -0500
Subject: [Users] Cactus Survey
Message-ID: <8A19FA31-ADA5-4DD7-B834-C0CB4CDDDDB4@cct.lsu.edu>

	
Dear Cactus users, 

We've designed a short survey to gather feedback on how you are using Cactus and Carpet, what we should be targeting for future development, and how to better support the use and development of Cactus applications and associated software. Please take a few minutes to fill this out; we really appreciate your comments.

http://surveymonkey.com/s.aspx?sm=S0g62YndjGMx1MPvMxW9fA%3d%3d

Thanks!

The Cactus Team

--
Gabrielle Allen
Associate Professor
Department of Computer Science
Louisiana State University
gallen at cct.lsu.edu