Am 21. September 2016 17:14:38 MESZ, schrieb Axel Huebl <a.huebl@hzdr.de>:
Alex,
The first parameter is simply
-s bash
as I wrote you in the previous mail.
Or for sake of simplicity:
tbg -s bash -c submit/0016gpus.cfg -t submit/bash/bash_mpirun.tpl ~/runs/testBatch06
Did you read the output of
tbg --help
yet?
Cheers,
Axel
On September 21, 2016 4:14:55 PM CEST, Alex Francisco <djlexes@gmail.com> wrote:
Dear developers PicOnGpu:
I'm running my simulation on my machine locally. when I execute the
line
how you say to me, the next form:
tbg -s /home/alex/paramSets/case001/submit/bash/ -c submit/0016gpus.cfg
-t
/home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl
~/runs/testBatch05
/home/alex/paramSets/case001/submit/bash/:
is a directory
Also, I try this comman.
tbg -s /home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl -c
submit/0016gpus.cfg -t
/home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl
~/runs/testBatch05
/home/alex/src/picongpu/src/tools/bin/tbg: línea 354:
/home/alex/paramSets/case001/submit/bash/bash_mpirun.tpl: permission
denied
I hope you can help me.
Thank you very much.
Alex.
2016-09-14 8:36 GMT-05:00 Huebl, Axel <a.huebl@hzdr.de>:
Dear Alex,
please read the output of
tbg --help
first. As any command in the unix/linux/mac world, the order of
parameters you specify behind it have a meaning that you need to
understand first.
a)
-s is the submit command
if you
are not on a cluster, run locally with -s bash
b) -t is a template to execute PIConGPU
if you are not on the cluster hypnos (which would be in our lab)
then use the other templates in submit/ such as bash/bash_mpirun.tpl
or
write your own.
Also before sending us error messages, please set your locale to
english
so we can understand them.
You can do so by running
export LC_ALL=en_US.UTF-8
before doing anything else. This will temporarily set the language to
english until you close your terminal (or SSH session) again.
Best regards,
Axel
On 11.09.2016 20:54, Alex Francisco wrote:
Dear developers PicOnGpu:
when i execute the line how you say to me, the next form:
tbg -s /home/alex/build/ -c submit/0016gpus.cfg -t
submit/hypnos/k20_profile.tpl ~/runs/testBatch01
This create this files in this directory
/home/alex/build/
alex@alex-Satellite-L635:~/build$ ls
CMake CMakeCache.txt CMakeFiles Show
and also create this folder: testBatch01
alex@alex-Satellite-L635:~/runs/testBatch02$ ls
picongpu tbg
All is alright, is it this the output of the simulation of example?
Thanks for your great help they have given me, and I hope your
answer
about my question.
Thank you very much.
Alex.
2016-08-28 6:47 GMT-05:00 Axel Huebl <a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de>>:
Hi Alex,
Are you even on a cluster with a batch system?
If yes, which one? PBS, Slurm, ...?
Otherwise, use -s bash and the -t submit/bash/...
"mpiexec"/"mpirun"
bash .tpl file for locsl runs.
Axel
On August 28, 2016 12:38:37 AM CEST, Alex Francisco
<djlexes@gmail.com <mailto:djlexes@gmail.com>> wrote:
Dear developers PicOnGpu:
I install the program again and I already are creating the
"bin"
folder
in
the directory ~ / ParamSet / case001
alex@alex-Satellite-L635:~/paramSets/case001$ ls
bin cmakeFlags include lib share submit
When I execute the netx instructions, show me this:
alex@alex-Satellite-L635:~/paramSets/case001$ tbg -s qsub -c
submit/0016gpus.cfg -t submit/hypnos/k20_profile.tpl
~/runs/testBatch01
/home/alex/src/picongpu/src/tools/bin/tbg: línea 354: qsub:
orden
no
encontrada
alex@alex-Satellite-L635:~/runs/testBatch01$
$PICSRC/configure
-i ~/paramSets/case002 ~/runs/testBatch01
cmake command: cmake
-DCMAKE_INSTALL_PREFIX=/home/alex/paramSets/case002
-DPIC_EXTENSION_PATH=/home/alex/runs/testBatch01
/home/alex/src/picongpu
-- Building libSplash version 1.4.0
-- Building RELEASE version
-- Parallel HDF5 found. Building parallel version
-- Building splashtools
-- Building splashtools parallel version
-- Configuring done
-- Generating done
-- Build files have been written to: /home/alex/src/picongpu
it is an error or that the order does not exist for the
instructions of
tbg
or qsub "wrong Fingered".
I hope can you help me,
Thank you very much.
Alex
2016-08-10 3:35 GMT-05:00 Garten, Marco <m.garten@hzdr.de
<mailto:m.garten@hzdr.de>>:
Did you perhaps execute the $PICSRC/configure command inside
your
home/alex/src/picongpu before? That will create some files
there
and
will
stop you
from compiling correctly.
First check if you have any changes in your source code:
cd ~/src/picongpu
git status
--> Please show us the output of this
If you have any modified or new files in there and NO
intentional
changes
you can do:
git reset --hard HEAD
That resets your local index and working tree to the state
of the
branch
as it was when you downloaded it. (Careful: it will also
delete
your
changes
if you made some)
Now you can retry building PIConGPU again:
rm -r ~/build/*
cd ~/build
$PICSRC/configure ~/paramSets/case001
make -j install
(please only do the make command inside the build directory
- if the
configure command writes to any other directory
than
build
that is a sign that something went wrong)
--> Please send us all the output until there again
Best,
Marco
Am Tue, 9 Aug 2016 16:50:05 -0500 schrieb Alex Francisco <
djlexes@gmail.com <mailto:djlexes@gmail.com>>:
alex@alex-Satellite-L635:~/src/picongpu$ ./configure
~/paramSets/case001
cmake command: cmake -DCUDA_ARCH=sm_20
-DCMAKE_INSTALL_PREFIX=/home/alex/paramSets/case001
-DPIC_EXTENSION_PATH=/home/alex/paramSets/case001 .
-- Building Debug
-- libSplash supports PARALLEL output
-- libSplash compiler definitions:
-D_LARGEFILE_SOURCE;-D_LARGEFILE64_SOURCE;-D_BSD_
SOURCE;-DENABLE_HDF5=1
-- Found 'adios_config': /usr/bin/adios_config
/usr/bin/adios_config: línea 121: pkgconfig: orden no
encontrada
-- The directory provided by 'adios_config -d' does not
exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES
ADIOS_INCLUDE_DIRS)
(Required is at least version "1.6.0")
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- Configuring done
-- Generating done
-- Build files have been written to:
/home/alex/src/picongpu
alex@alex-Satellite-L635:~/src/picongpu$ make -j
[100%] Built target splash2txt
alex@alex-Satellite-L635:~/src/picongpu$ make install
[100%] Built target splash2txt
Install the project...
-- Install configuration: "Debug"
-- Up-to-date: /home/alex/paramSets/case001/./splash2txt
alex@alex-Satellite-L635:~/src/picongpu$ cd
~/paramSets/case001/
alex@alex-Satellite-L635:~/paramSets/case001$ ls
cmakeFlags include splash2txt submit
2016-08-09 16:37 GMT-05:00 Alex Francisco
<djlexes@gmail.com
<mailto:djlexes@gmail.com>>:
alex@alex-Satellite-L635:~/build$ make -j install
make: *** No rule to make target 'install'. Alto.
alex@alex-Satellite-L635:~/build$ make -j
make: *** No se especificó ningún objetivo y no se
encontró
ningún
makefile. Alto.
2016-08-09 16:35 GMT-05:00 Alex Francisco
<djlexes@gmail.com
<mailto:djlexes@gmail.com>>:
alex@alex-Satellite-L635:~/build$
~/src/picongpu/./configure
~/paramSets/case001/
cmake command: cmake -DCUDA_ARCH=sm_20
-DCMAKE_INSTALL_PREFIX=/home/a
lex/paramSets/case001/
-DPIC_EXTENSION_PATH=/home/alex/paramSets/case001/
/home/alex/src/picongpu/.
-- Building Debug
-- libSplash supports PARALLEL output
-- libSplash compiler definitions:
-D_LARGEFILE_SOURCE;-D_LARGEFI
LE64_SOURCE;-D_BSD_SOURCE;-DENABLE_HDF5=1
-- Found 'adios_config': /usr/bin/adios_config
/usr/bin/adios_config: línea 121: pkgconfig: orden no
encontrada
-- The directory provided by 'adios_config -d' does not
exist:
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES
ADIOS_INCLUDE_DIRS)
(Required is at least version "1.6.0")
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- program_options
-- regex
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the
project:
PIC_EXTENSION_PATH
-- Build files have been written to:
/home/alex/src/picongpu
alex@alex-Satellite-L635:~/build$ make -j intall
make: *** No rule to make target 'intall'. Alto.
alex@alex-Satellite-L635:~/build$
2016-08-09 16:17 GMT-05:00 Marco Garten <m.garten@hzdr.de
<mailto:m.garten@hzdr.de>>:
This still looks like as if your compile process has not
been
successful
and the executable has not been built (nor has the bin
folder
been
created).
Could you please remove all the contents inside the
~/build
directory,
repeat the following steps and show us all the output
from
your
terminal?
1. Configure the example (cd ~/build &&
$PICSRC/configure
~/paramSets/case001)
2. Compile the code (make -j install)
Hope we can get your code running soon!
Best,
Marco
Am 09.08.2016 um 22:34 schrieb Alex Francisco:
When I execute this line|: |
tbg -s qsub -c ~/paramSets/case001/submit/0016gpus.cfg
-t
~/paramSets/case001/submit/hypnos/k20_profile.tpl
~/runs/testBatch01
Show me this in my terminal:
alex@alex-Satellite-L635:~/paramSets/case001$ tbg -s
qsub
-c
~/paramSets/case001/submit/0016gpus.cfg -t
~/paramSets/case001/submit/hypnos/k20_profile.tpl
~/runs/testBatch01
cp: no se puede efectuar `stat' sobre
«/home/alex/paramSets/case001/bin»: No existe el
archivo o
el
directorio
/home/alex/src/picongpu/src/tools/bin/tbg: línea 354:
qsub:
orden no
encontrada
thank you very much,
I hope you can help me,
Alex.
2016-08-09 13:36 GMT-05:00 Huebl, Axel
<a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>>>:
Your simulation has not yet run.
Please check the output of the "tbg" command, the
"queue"
of your
batch
system, etc.
if it would have run, a "simOutput" dir would
exist in
the
directory you
listed.
Best,
Axel
On 09.08.2016 12:49, Alex Francisco wrote:
which is the output of the example simulation
"Laser
Wakefield"?,.
I can see is this in my folder
~/runs/testBatch01:
alex@alex-Satellite-L635:~/runs/testBatch01$ ls
picongpu tbg
Thank you very much
Alex.
2016-08-09 11:27 GMT-05:00 René Widera
<r.widera@hzdr.de <mailto:r.widera@hzdr.de>
<mailto:r.widera@hzdr.de
<mailto:r.widera@hzdr.de>>
<mailto:r.widera@hzdr.de
<mailto:r.widera@hzdr.de>
<mailto:r.widera@hzdr.de <mailto:r.widera@hzdr.de>>>>:
Dear Alex,
`make install` for splash2txt copies the
binary to
the
folder
defined in `CMAKE_INSTALL_PREFIX`.
It not creates a `bin` folder.
René
On 09.08.2016 17:48, Alex Francisco wrote:
When I execute: |make install, ||it is
not
copying the
binaries
/bin to
this folder, |
alex@alex-Satellite-L635:~/paramSets/case001$
ls
cmakeFlags include splash2txt submit
also when I am in the folder
~/src/picongpu,
show
me
this,
when I
execute cmake -L:
alex@alex-Satellite-L635:~/src/picongpu$
cmake -L
*CMake Error: The source
"/home/alex/src/picongpu/CMakeLists.txt"
does
not match the source
"/home/alex/src/picongpu/src/
tools/splash2txt/CMakeLists.txt"
used to
generate
cache. Re-run cmake with a
different
source
directory.*
-- Cache values
ADIOS_CONFIG:FILEPATH=/usr/bin/adios_config
CMAKE_BUILD_TYPE:STRING=Debug
CMAKE_INSTALL_PREFIX:PATH=/home/alex/paramSets/case001
HDF5_DIR:PATH=HDF5_DIR-NOTFOUND
MPI_EXTRA_LIBRARY:STRING=/usr/lib/libmpi.so;/usr/lib/x86_64-
linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
MPI_LIBRARY:FILEPATH=/usr/lib/libmpi_cxx.so
Splash_LIBRARIES:FILEPATH=/home/alex/lib/splash/lib/libsplash.a
Splash_ROOT_DIR:PATH=/home/alex/lib/splash
2016-08-08 15:41 GMT-05:00 Marco Garten
<
m.garten@hzdr.de <mailto:m.garten@hzdr.de>
<mailto:m.garten@hzdr.de
<mailto:m.garten@hzdr.de>>
<mailto:m.garten@hzdr.de
<mailto:m.garten@hzdr.de>
<mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>
<mailto:m.garten@hzdr.de
<mailto:m.garten@hzdr.de>
<mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>
<mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>
<mailto:m.garten@hzdr.de <mailto:m.garten@hzdr.de>>>>>:
Dear Alex,
the TBG command as you executed it
uses
the
relative
path
from inside
your paramSet. The config file is
located
inside
~/paramSets/case001/submit - just
like the
hardware
template
file
k20_profile.tpl is in
~/paramSets/case001/submit/hyp
nos/.
So either execute the command from
~/paramSets/case001 or
use the
absolute path.
Don't forget to delete the folder
~/runs/testBatch01/
before
because
otherwise TBG will tell you that the
job
name
is
already in
use. (The
run folders all contain a copy of
the
executable
and
the
parameter set
regardless if the job is running or
not)
You seem to be using the config
files and
the
architecture
template of
our home cluster on your local
machine,
though.
That
would
require you
to have 16 GPUs if you use the
0016gpus.cfg
file.
If
you
want to do a
quick test whether the code is
running at
all
you
can just
execute:
cd ~/paramSets/case001/bin
./picongpu -d 1 1 1 -g 64 128 64 -s
1000
This will run the code with one
GPU
on a
grid
of
64 x
128 x
64 cells for
1000 steps.
Please look at any of the *gpus.cfg
files
for
additional
options to the
command that will generate output. I
would
recommend
something like:
--png_e.period 50 --png_e.axis yz
--png_e.slicePoint
0.5
--png_e.folder
pngElectronsYZ --elec_cnt.period 50
This will give you the total count
of
electrons in
the
simulation at
every 50th time step and also a PNG
showing a
YZ
slice of
the electron
charge density. The output will now
be
created
directly in
the "bin"
folder where your executable is.
Hope this works for you!
Best,
Marco
Am 08.08.2016 um 18:14 schrieb Alex
Francisco:
Thank you very much this worked!!!
When I do execute this line of
code in
my
terminal
show this:
alex@alex-Satellite-L635:~/
src/picongpu$
tbg -s
qsub -c
submit/0016gpus.cfg -t
~/paramSets/case001/submit/
hypnos/k20_profile.tpl
~/runs/testBatch01/
The given cfg file
"submit/0016gpus.cfg"
does not
exist
(-c|--cfg).
However, I turn to the folder
case001
and
there
show me
the folder
testBatch01, I ask to yours, if it
can
be
showing
me
this
because I once
create and do not need to recreate
the
subfolder
(testBatch01) ??
alex@alex-Satellite-L635:~/runs$
ls
testBatch01
and in the folder testBatch01 show
me
this
files:
alex@alex-Satellite-L635:~/runs/testBatch01$ ls
picongpu tbg
Furthermore, as I view the
simulation
output?
I hope you can help me.
Thank you very much.
Alex Estupiñán.
2016-08-06 11:33 GMT-05:00 Huebl,
Axel
<a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>>
<mailto:a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de> <mailto:a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de>>>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>>
<mailto:a.huebl@hzdr.de <mailto:
a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>>>>
<mailto:a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de>>>
<mailto:a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de> <mailto:a.huebl@hzdr.de
<mailto:a.huebl@hzdr.de>>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>
<mailto:a.huebl@hzdr.de <mailto:a.huebl@hzdr.de>>>>>>:
I also fixed that compile
problem in
splash2txt
by now.
https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>>
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>>>
<https://github.com/ComputationalRadiationPhysics/picongpu/
<https://github.com/ComputationalRadiationPhysics/picongpu/>
pull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/
<https://github.com/ComputationalRadiationPhysics/picongpu/>
pull/1545>
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>>
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545
<https://github.com/ComputationalRadiationPhysics/picongpu/p
<https://github.com/ComputationalRadiationPhysics/picongpu/p>
ull/1545>>>>
You can just remove or comment
out
via
"//"
the line
that is causing the
error.
Axel
On 06.08.2016 11:07, Axel
Huebl
wrote:
Dear Alex,
You don't need to build the
helper
tool in
post-processing,
splash2txt for now. Just skip
step
6.
Otherwise: please make sure
the
source code
is
unmodified. For
compile errors, please report
compiler
version,
cmake
version, cmake
-L . output and ubuntu
version.
Compile issues are also best
tracked
in our
github
since we can
assign, track, link and
archive it
there.
Axel
On August 6, 2016 10:56:09
AM EDT,
"Bussmann, Dr.
Michael (FWKT) -
4167" <m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de>
<mailto:m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de>>
<mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>
<mailto:m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de>
<mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>
<mailto:m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de>
<mailto:m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>>>
<mailto:m.bussmann@hzdr.de
<mailto:m.bussmann@hzdr.de> <mailto:
m.bussmann@hzdr.de <mailto:m.bussmann@hzdr.de>>
<mailto:m.bussmann@hzd