[Users] ETK in Carver

Sat Mar 10 06:10:13 CST 2012

Jose

When you tried bash, how did you switch to bash? Could you try (just
to debug things) to switch your account to bash using NIM, and then
building again from scratch?

-erik

On Thu, Mar 8, 2012 at 12:12 AM, Jose Fiestas Iquira <jafiestas at lbl.gov> wrote:
> Hi Erik,
>
> I am using csh, but I tried the same steps using bash, and got the same
> error.
>
> I realized, in hopper.ini there are some module commands, but not in
> queenbee.ini. I ask me why are they necessary in Hopper.
>
> Would be a way to look into your directory in Hopper and try it there?
> Probably I can see the difference. Or that you look into my directory?:
>
> /global/u1/f/fiestas/CACTUS/Cactus
>
> I opened the permissions there.
>
> Thanks,
> Jose
>
>
> On Wed, Mar 7, 2012 at 7:17 PM, Erik Schnetter <schnetter at cct.lsu.edu>
> wrote:
>>
>> Jose
>>
>> Another idea. What shell do you use? I use bash.
>>
>> -erik
>>
>> On Wed, Mar 7, 2012 at 8:33 PM, Jose Fiestas Iquira <jafiestas at lbl.gov>
>> wrote:
>> > Dear Colleagues,
>> > I am trying to install ETK in hopper, at NERSC. I started from scratch
>> > following the steps of the advanced tutorial. I am building a package,
>> > which
>> > includes an N-body code and Cactus, so I my aim is to be able to run
>> > Cactus
>> > in different machines. My last attempt showed me following issue:
>> > After doing simfactory/bin/sim setup in hopper, I tried
>> >
>> > simfactory/bin/sim build
>> >
>> > with the result
>> >
>> > Using configuration: sim
>> > Reconfiguring sim
>> > Writing configuration to:
>> > /global/u1/f/fiestas/CACTUS-save/Cactus/configs/sim/OptionList
>> > /bin/bash: module: command not found
>> >
>> > I am using the last development version here
>> > http://einsteintoolkit.org/download/ (also tried the last release with
>> > the
>> > same results)
>> >
>> > I found in simfactory/mdb/machines/hopper.ini a list of module commands
>> > which apparently can not be executed. I run it in queenbee without
>> > problems.
>> > Would appreciate any help.
>> >
>> > Regards,
>> > Jose
>> >
>> >
>> >
>> >
>> > On Sat, Feb 25, 2012 at 11:51 AM, Jose Fiestas Iquira
>> > <jafiestas at lbl.gov>
>> > wrote:
>> >>
>> >> Hi Erik,
>> >>
>> >> Yes, should be loaded automatically. Find strange they don't.
>> >> I use ./simfactory/bin/sim build from the Cactus directory (I tried
>> >> adding --thornlist=manifest/einsteintoolkit.th) but I keep getting
>> >> Using configuration: sim
>> >> Reconfiguring sim
>> >> Writing configuration to:
>> >> /global/u1/f/fiestas/CACTUS/Cactus/configs/sim/OptionList
>> >> /bin/bash: module: command not found
>> >>
>> >> I tried deleting the module commands
>> >> in simfactory/mdb/machines/hopper.ini
>> >> and doing them by hand.
>> >> I got more output (attached) but an error anyway.
>> >>
>> >> This tries are from scratch, I loaded ETK from
>> >> http://einsteintoolkit.org/download/
>> >> the development version, as you tried.
>> >>
>> >> It seems to me the problem is related to the configuration of my
>> >> account.
>> >> But I did not change the defaults.
>> >>
>> >> Best,
>> >> Jose
>> >>
>> >>
>> >> On Sat, Feb 25, 2012 at 6:16 AM, Erik Schnetter <schnetter at cct.lsu.edu>
>> >> wrote:
>> >>>
>> >>> Jose
>> >>>
>> >>> The modules that are loaded automatically should not matter;
>> >>> Simfactory should do the right thing anyway.
>> >>>
>> >>> What command do you use to compile? I use
>> >>>
>> >>> ./bin/sim build --thornlist=manifest/einsteintoolkit.th
>> >>>
>> >>> -erik
>> >>>
>> >>> On Fri, Feb 24, 2012 at 6:36 PM, Jose Fiestas Iquira
>> >>> <jafiestas at lbl.gov>
>> >>> wrote:
>> >>> > Sorri pgi compilers, not pig :)
>> >>> >
>> >>> >
>> >>> > On Fri, Feb 24, 2012 at 3:35 PM, Jose Fiestas Iquira
>> >>> > <jafiestas at lbl.gov>
>> >>> > wrote:
>> >>> >>
>> >>> >> You have loaded the pig compilers. I tried both pig and intel
>> >>> >> without
>> >>> >> success. It is something related to the configuration. I get:
>> >>> >> Internal error - couldn't enter
>> >>> >> '/global/u1/f/fiestas/CACTUS/Cactus/configs/sim/config-data'
>> >>> >>
>> >>> >> Cheers,
>> >>> >> Jose
>> >>> >>
>> >>> >>
>> >>> >> On Fri, Feb 24, 2012 at 3:30 PM, Erik Schnetter
>> >>> >> <schnetter at cct.lsu.edu>
>> >>> >> wrote:
>> >>> >>>
>> >>> >>> $ module list
>> >>> >>> Currently Loaded Modulefiles:
>> >>> >>>  1) modules/3.2.6.6
>> >>> >>>  2) xtpe-network-gemini
>> >>> >>>  3) pgi/11.9.0
>> >>> >>>  4) xt-libsci/11.0.03
>> >>> >>>  5) udreg/2.3.1-1.0400.3911.5.13.gem
>> >>> >>>  6) ugni/2.3-1.0400.4127.5.20.gem
>> >>> >>>  7) pmi/3.0.0-1.0000.8661.28.2807.gem
>> >>> >>>  8) dmapp/3.2.1-1.0400.3965.10.63.gem
>> >>> >>>  9) gni-headers/2.1-1.0400.4156.6.1.gem
>> >>> >>>  10) xpmem/0.1-2.0400.30792.5.6.gem
>> >>> >>>  11) xe-sysroot/4.0.36
>> >>> >>>  12) xt-asyncpe/5.04
>> >>> >>>  13) atp/1.3.0
>> >>> >>>  14) PrgEnv-pgi/4.0.36
>> >>> >>>  15) eswrap/1.0.10
>> >>> >>>  16) xtpe-mc12
>> >>> >>>  17) xt-shmem/5.4.0
>> >>> >>>  18) xt-mpich2/5.4.0
>> >>> >>>  19) torque/2.5.9
>> >>> >>>  20) moab/6.1.4
>> >>> >>>
>> >>> >>> -erik
>> >>> >>>
>> >>> >>> On Fri, Feb 24, 2012 at 4:31 PM, Jose Fiestas Iquira
>> >>> >>> <jafiestas at lbl.gov>
>> >>> >>> wrote:
>> >>> >>> > Erik,
>> >>> >>> > I suspect the default modules I loaded are not sufficient,
>> >>> >>> > because
>> >>> >>> > I am
>> >>> >>> > not
>> >>> >>> > doing more than 'simfactory/bin/sim setup'
>> >>> >>> > and  'simfactory/bin/sim
>> >>> >>> > build'.
>> >>> >>> > Could you please send me a 'module list' of your account to
>> >>> >>> > compare
>> >>> >>> > with
>> >>> >>> > mine?
>> >>> >>> > Best,
>> >>> >>> > Jose
>> >>> >>> >
>> >>> >>> >
>> >>> >>> > On Fri, Feb 24, 2012 at 12:26 PM, Erik Schnetter
>> >>> >>> > <schnetter at cct.lsu.edu>
>> >>> >>> > wrote:
>> >>> >>> >>
>> >>> >>> >> Jose
>> >>> >>> >>
>> >>> >>> >> I just built the ET from scratch and ran the test cases there.
>> >>> >>> >> All
>> >>> >>> >> went fine on Hopper, no problems at all.
>> >>> >>> >>
>> >>> >>> >> -erik
>> >>> >>> >>
>> >>> >>> >> On Fri, Feb 24, 2012 at 2:39 PM, Erik Schnetter
>> >>> >>> >> <schnetter at cct.lsu.edu>
>> >>> >>> >> wrote:
>> >>> >>> >> > On Fri, Feb 24, 2012 at 2:11 PM, Jose Fiestas Iquira
>> >>> >>> >> > <jafiestas at lbl.gov>
>> >>> >>> >> > wrote:
>> >>> >>> >> >> Hi Erik,
>> >>> >>> >> >>
>> >>> >>> >> >> I am getting in Hopper the same error after
>> >>> >>> >> >> simfactory/bin/sim
>> >>> >>> >> >> build:
>> >>> >>> >> >> Using configuration: sim
>> >>> >>> >> >> Reconfiguring sim
>> >>> >>> >> >> Writing configuration to:
>> >>> >>> >> >> /global/u1/f/fiestas/CACTUS/Cactus/configs/sim/OptionList
>> >>> >>> >> >> /bin/bash: module: command not found
>> >>> >>> >> >> fiestas at hopper10:~/CACTUS/Cactus> exit
>> >>> >>> >> >> exit
>> >>> >>> >> >>
>> >>> >>> >> >> Could you install it without problems?
>> >>> >>> >> >
>> >>> >>> >> > Yes. I am not seeing these problems. Maybe they are specific
>> >>> >>> >> > to
>> >>> >>> >> > your
>> >>> >>> >> > account settings? Could you investigate where the "module"
>> >>> >>> >> > command
>> >>> >>> >> > is
>> >>> >>> >> > used?
>> >>> >>> >> >
>> >>> >>> >> >> A question. Should I set hopper10 as:
>> >>> >>> >> >> key allocation []
>> >>> >>> >> >
>> >>> >>> >> > I don't know what you mean by this.
>> >>> >>> >> >
>> >>> >>> >> > The allocation on Hopper is the "repository" there; it is
>> >>> >>> >> > e.g.
>> >>> >>> >> > "m152"
>> >>> >>> >> > for me.
>> >>> >>> >> >
>> >>> >>> >> > -erik,
>> >>> >>> >> >
>> >>> >>> >> >> Thanks,
>> >>> >>> >> >> Jose
>> >>> >>> >> >>
>> >>> >>> >> >>
>> >>> >>> >> >> On Fri, Feb 24, 2012 at 10:45 AM, Jose Fiestas Iquira
>> >>> >>> >> >> <jafiestas at lbl.gov>
>> >>> >>> >> >> wrote:
>> >>> >>> >> >>>
>> >>> >>> >> >>> You mean this version?
>> >>> >>> >> >>>
>> >>> >>> >> >>>
>> >>> >>> >> >>>
>> >>> >>> >> >>> http://svn.einsteintoolkit.org/manifest/trunk/einsteintoolkit.th
>> >>> >>> >> >>>
>> >>> >>> >> >>> I am trying now in a new directory. I had installed Cactus,
>> >>> >>> >> >>> the
>> >>> >>> >> >>> Wavetoy
>> >>> >>> >> >>> and ETk in the same place and probably there were some
>> >>> >>> >> >>> conflicts.
>> >>> >>> >> >>> That
>> >>> >>> >> >>> is
>> >>> >>> >> >>> where I got the module error. Hope doing it new works well
>> >>> >>> >> >>> as
>> >>> >>> >> >>> in
>> >>> >>> >> >>> your
>> >>> >>> >> >>> case.
>> >>> >>> >> >>> Did you follow the tutorial in the ETK page for new users?
>> >>> >>> >> >>>
>> >>> >>> >> >>> Cheers,
>> >>> >>> >> >>> Jose
>> >>> >>> >> >>>
>> >>> >>> >> >>>
>> >>> >>> >> >>>
>> >>> >>> >> >>>
>> >>> >>> >> >>> On Fri, Feb 24, 2012 at 10:18 AM, Erik Schnetter
>> >>> >>> >> >>> <schnetter at cct.lsu.edu>
>> >>> >>> >> >>> wrote:
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> Jose
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> No, things didn't work on Carver. I received errors, but
>> >>> >>> >> >>>> didn't
>> >>> >>> >> >>>> investigate, mostly because I dislike the PGI compiler.
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> I'm building on Hopper as we speak, using the Intel
>> >>> >>> >> >>>> compiler,
>> >>> >>> >> >>>> and
>> >>> >>> >> >>>> things are going fine.
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> I'm using the development version of the ET, not the
>> >>> >>> >> >>>> release
>> >>> >>> >> >>>> from
>> >>> >>> >> >>>> last
>> >>> >>> >> >>>> autumn, though.
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> -erik
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> On Fri, Feb 24, 2012 at 12:40 PM, Jose Fiestas Iquira
>> >>> >>> >> >>>> <jafiestas at lbl.gov>
>> >>> >>> >> >>>> wrote:
>> >>> >>> >> >>>> > Hi Erik,
>> >>> >>> >> >>>> > The problem with module (?) came actually when I tried
>> >>> >>> >> >>>> > it
>> >>> >>> >> >>>> > in
>> >>> >>> >> >>>> > Hopper.
>> >>> >>> >> >>>> > There
>> >>> >>> >> >>>> > is no special need for Carver, Hopper would be fine. Did
>> >>> >>> >> >>>> > your
>> >>> >>> >> >>>> > try
>> >>> >>> >> >>>> > in
>> >>> >>> >> >>>> > Carver
>> >>> >>> >> >>>> > worked, anyway?
>> >>> >>> >> >>>> > Best,
>> >>> >>> >> >>>> > Jose
>> >>> >>> >> >>>> >
>> >>> >>> >> >>>> >
>> >>> >>> >> >>>> > On Fri, Feb 24, 2012 at 9:14 AM, Erik Schnetter
>> >>> >>> >> >>>> > <schnetter at cct.lsu.edu>
>> >>> >>> >> >>>> > wrote:
>> >>> >>> >> >>>> >>
>> >>> >>> >> >>>> >> On Wed, Feb 22, 2012 at 8:38 PM, Jose Fiestas Iquira
>> >>> >>> >> >>>> >> <jafiestas at lbl.gov>
>> >>> >>> >> >>>> >> wrote:
>> >>> >>> >> >>>> >> > It was like these:
>> >>> >>> >> >>>> >> > ....
>> >>> >>> >> >>>> >> > COMPILING
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > /global/u1/f/fiestas/CACTUS/Cactus/arrangements/Carpet/LoopControl/src/loopcontrol.c
>> >>> >>> >> >>>> >> > PGC-W-0155-parallel for loop variable must be local k
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > (/global/u1/f/fiestas/CACTUS/Cactus/configs/sim/build/LoopControl/loopcontrol.c:
>> >>> >>> >> >>>> >> > 1080)
>> >>> >>> >> >>>> >> > PGC-S-0094-Illegal type conversion required
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > (/global/u1/f/fiestas/CACTUS/Cactus/configs/sim/build/LoopControl/loopcontrol.c:
>> >>> >>> >> >>>> >> > 1080)
>> >>> >>> >> >>>> >> > PGC-S-0094-Illegal type conversion required
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > (/global/u1/f/fiestas/CACTUS/Cactus/configs/sim/build/LoopControl/loopcontrol.c:
>> >>> >>> >> >>>> >> > 1080)
>> >>> >>> >> >>>> >> > PGC/x86-64 Linux 9.0-3: compilation completed with
>> >>> >>> >> >>>> >> > severe
>> >>> >>> >> >>>> >> > errors
>> >>> >>> >> >>>> >> > make[3]: *** [loopcontrol.c.o] Error 2
>> >>> >>> >> >>>> >> > make[2]: *** [make.checked] Error 2
>> >>> >>> >> >>>> >> > make[1]: ***
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > [/global/u1/f/fiestas/CACTUS/Cactus/configs/sim/lib/libthorn_LoopControl.a]
>> >>> >>> >> >>>> >> > Error 2
>> >>> >>> >> >>>> >> > make[1]: *** Waiting for unfinished jobs....
>> >>> >>> >> >>>> >> > .....
>> >>> >>> >> >>>> >> > COMPILING
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > /global/u1/f/fiestas/CACTUS/Cactus/arrangements/EinsteinInitialData/IDAxiBrillBH/src/ParamCheck.c
>> >>> >>> >> >>>> >> > Creating
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > /global/u1/f/fiestas/CACTUS/Cactus/configs/sim/lib/libthorn_IDAnalyticBH.a
>> >>> >>> >> >>>> >> > Creating
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > /global/u1/f/fiestas/CACTUS/Cactus/configs/sim/lib/libthorn_IDAxiBrillBH.a
>> >>> >>> >> >>>> >> > Creating
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > /global/u1/f/fiestas/CACTUS/Cactus/configs/sim/lib/libthorn_IDAxiOddBrillBH.a
>> >>> >>> >> >>>> >> > make: *** [sim] Error 2
>> >>> >>> >> >>>> >> >
>> >>> >>> >> >>>> >> > I am trying hopper now. Let see.
>> >>> >>> >> >>>> >>
>> >>> >>> >> >>>> >> Is there a reason why you want to use Carver, or would
>> >>> >>> >> >>>> >> another
>> >>> >>> >> >>>> >> machine
>> >>> >>> >> >>>> >> be fine as well?
>> >>> >>> >> >>>> >>
>> >>> >>> >> >>>> >> The PGI compilers are often a bit peculiar; I prefer
>> >>> >>> >> >>>> >> the
>> >>> >>> >> >>>> >> Intel
>> >>> >>> >> >>>> >> compilers. Let me try to build on Hopper -- this should
>> >>> >>> >> >>>> >> work
>> >>> >>> >> >>>> >> fine,
>> >>> >>> >> >>>> >> I
>> >>> >>> >> >>>> >> can then help you there.
>> >>> >>> >> >>>> >>
>> >>> >>> >> >>>> >> -erik
>> >>> >>> >> >>>> >>
>> >>> >>> >> >>>> >> --
>> >>> >>> >> >>>> >> Erik Schnetter <schnetter at cct.lsu.edu>
>> >>> >>> >> >>>> >> http://www.perimeterinstitute.ca/personal/eschnetter/
>> >>> >>> >> >>>> >
>> >>> >>> >> >>>> >
>> >>> >>> >> >>>>
>> >>> >>> >> >>>>
>> >>> >>> >> >>>>
>> >>> >>> >> >>>> --
>> >>> >>> >> >>>> Erik Schnetter <schnetter at cct.lsu.edu>
>> >>> >>> >> >>>> http://www.perimeterinstitute.ca/personal/eschnetter/
>> >>> >>> >> >>>
>> >>> >>> >> >>>
>> >>> >>> >> >>
>> >>> >>> >> >
>> >>> >>> >> >
>> >>> >>> >> >
>> >>> >>> >> > --
>> >>> >>> >> > Erik Schnetter <schnetter at cct.lsu.edu>
>> >>> >>> >> > http://www.perimeterinstitute.ca/personal/eschnetter/
>> >>> >>> >>
>> >>> >>> >>
>> >>> >>> >>
>> >>> >>> >> --
>> >>> >>> >> Erik Schnetter <schnetter at cct.lsu.edu>
>> >>> >>> >> http://www.perimeterinstitute.ca/personal/eschnetter/
>> >>> >>> >
>> >>> >>> >
>> >>> >>>
>> >>> >>>
>> >>> >>>
>> >>> >>> --
>> >>> >>> Erik Schnetter <schnetter at cct.lsu.edu>
>> >>> >>> http://www.perimeterinstitute.ca/personal/eschnetter/
>> >>> >>
>> >>> >>
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>> Erik Schnetter <schnetter at cct.lsu.edu>
>> >>> http://www.perimeterinstitute.ca/personal/eschnetter/
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> Erik Schnetter <schnetter at cct.lsu.edu>
>> http://www.perimeterinstitute.ca/personal/eschnetter/
>
>

-- 
Erik Schnetter <schnetter at cct.lsu.edu>
http://www.perimeterinstitute.ca/personal/eschnetter/