Re: [Users] Problem with compiling Einstein Toolkit on Cray system

2016-09-16 Thread L.S. Oswald 
Ok, useful to know! Many thanks to everyone who's emailed me with help: 
I got considerably further with attempting to compile the Einstein 
Toolkit and whilst I haven't actually been successful yet (and have run 
out of time at this particular point to continue trying) I've certainly 
learned a lot about compiling.

Next time I try I'll have a go at getting an account on Queen Bee 2.

Best wishes and thanks again,

Lucy

On 2016-09-13 6:24 pm, Frank Loeffler wrote:
> On Tue, Sep 13, 2016 at 05:02:09PM +0200, L.S. Oswald wrote:
>> In fact that's what I tried originally, but I realised the commands 
>> only
>> work if you're compiling on Queen Bee, not any other supercomputer.
>> Google tells me that the Queen Bee supercomputer has been retired, so 
>> I
>> wouldn't be able to obtain an account on it in any case.
> 
> Google is right, but what we mean when referring to "Queen Bee" 
> nowadays
> is "Queen Bee 2":
> 
>   http://www.hpc.lsu.edu/resources/hpc/system.php?system=QB2
> 
> We should be better about including the '2'.
> 
> Frank
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Re: [Users] Problem with compiling Einstein Toolkit on Cray system

2016-09-13 Thread Frank Loeffler 
On Tue, Sep 13, 2016 at 05:02:09PM +0200, L.S. Oswald wrote:
> In fact that's what I tried originally, but I realised the commands only 
> work if you're compiling on Queen Bee, not any other supercomputer. 
> Google tells me that the Queen Bee supercomputer has been retired, so I 
> wouldn't be able to obtain an account on it in any case.

Google is right, but what we mean when referring to "Queen Bee" nowadays
is "Queen Bee 2":

  http://www.hpc.lsu.edu/resources/hpc/system.php?system=QB2

We should be better about including the '2'.

Frank

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Re: [Users] Problem with compiling Einstein Toolkit on Cray system

2016-09-13 Thread L.S. Oswald 
In fact that's what I tried originally, but I realised the commands only 
work if you're compiling on Queen Bee, not any other supercomputer. 
Google tells me that the Queen Bee supercomputer has been retired, so I 
wouldn't be able to obtain an account on it in any case.

Lucy

On 2016-09-12 4:33 pm, Erik Schnetter wrote:
> Lucy
> 
> Have you tried using the Einstein Toolkit on Queen Bee, as suggested
> here  [4]>?
> 
> -erik
> 
> On Tue, Sep 6, 2016 at 11:56 AM, L.S. Oswald  wrote:
> 
>> Dear Erik
>> 
>> In general I've been using the commands at
>> 
> https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users
>> [1]. I have tried configuring with the debian.cfg file and also
>> attempted creating my own configuration file. Moving onto a
>> different computer solved my MPI issue but produced a new error,
>> which I've written about in my reply to Rahul. I'm afraid I don't
>> know what type of computer I'm using now but I should be able to
>> find out tomorrow.
>> 
>> Hopefully my other email gives an overview of my latest problem. I
>> attach the full log of the output received when building the
>> toolkit.
>> 
>> Many thanks for your help,
>> 
>> Lucy
>> 
>> On 2016-09-06 5:41 pm, Erik Schnetter wrote:
>> 
>> Lucy
>> 
>> The Simulation Factory has several example option lists for Cray
>> systems; look e.g. at bluewaters or edison. I don't recommend
>> changing
>> the "config-info" file, since this file will be overwritten.
>> Instead,
>> you can set such options in your option list.
>> 
>> If you need more help, then we'll need more details: What kind of
>> Cray
>> system is this? What options did you pass when you configured the
>> Einstein Toolkit? What output did you receive while configuring?
>> etc.
>> 
>> -erik
>> 
>> On Mon, Aug 29, 2016 at 12:47 PM, L.S. Oswald 
>> wrote:
>> 
>> Hello
>> 
>> I'm attempting to install the Einstein Toolkit on Dora, which is a
>> Cray
>> system supercomputer. In doing so I came across the following
>> error:
>> 
>> Configuration script for thorn MPI returned exit code 5
>> Error message: 'MPI could not be configured: neither
>> automatic nor
>> manual configuration succeeded'
>> 
>> In addition the log stated that:
>> No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR =
>> /usr)
>> 
>> I subsequently discovered that it was looking in the wrong place
>> for the
>> MPI root directory and that the reason it was looking under /usr
>> instead
>> of /opt/cray/mpt/7.3.2/gni/mpich-cray/8.3 was because that was the
>> setting in the ubuntu configuration file that I had used when
>> configuring SimFactory. On a reattempt therefore I did not use the
>> ubuntu.cfg file when configuring SimFactory, and got the following
>> error
>> instead:
>> 
>> Configuring with flesh MPI
>> Warning: use of flesh MPI via MPI option is deprecated and
>> should be replaced with the thorn ExternalLibraries/MPI and its
>> MPI_DIR
>> option
>> MPI selected, but no known MPI method - what is
>> "/opt/cray/mpt/7.3.2/gni/mpich-cray/8.3" ?
>> 
>> Attempts at altering the Makefile and the config-info file resulted
>> in
>> either no change, or more errors.
>> 
>> Please would you be able to advise me on the correct way to specify
>> the
>> root directory for MPI?
>> 
>> Many thanks,
>> 
>> Lucy Oswald
>> ___
>> Users mailing list
>> Users@einsteintoolkit.org
>> http://lists.einsteintoolkit.org/mailman/listinfo/users [2] [1]
>> 
>> --
>> 
>> Erik Schnetter 
>> http://www.perimeterinstitute.ca/personal/eschnetter/ [3] [2]
>> 
>> Links:
>> --
>> [1] http://lists.einsteintoolkit.org/mailman/listinfo/users [2]
>> [2] http://www.perimeterinstitute.ca/personal/eschnetter/ [3]
> 
> --
> 
> Erik Schnetter 
> http://www.perimeterinstitute.ca/personal/eschnetter/ [3]
> 
> Links:
> --
> [1] 
> https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users
> [2] http://lists.einsteintoolkit.org/mailman/listinfo/users
> [3] http://www.perimeterinstitute.ca/personal/eschnetter/
> [4] https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users
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Re: [Users] Problem with compiling Einstein Toolkit on Cray system

2016-09-06 Thread L.S. Oswald 

Dear Erik

In general I've been using the commands at 
https://docs.einsteintoolkit.org/et-docs/Simplified_Tutorial_for_New_Users. 
I have tried configuring with the debian.cfg file and also attempted 
creating my own configuration file. Moving onto a different computer 
solved my MPI issue but produced a new error, which I've written about 
in my reply to Rahul. I'm afraid I don't know what type of computer I'm 
using now but I should be able to find out tomorrow.


Hopefully my other email gives an overview of my latest problem. I 
attach the full log of the output received when building the toolkit.


Many thanks for your help,

Lucy

On 2016-09-06 5:41 pm, Erik Schnetter wrote:

Lucy

The Simulation Factory has several example option lists for Cray
systems; look e.g. at bluewaters or edison. I don't recommend changing
the "config-info" file, since this file will be overwritten. Instead,
you can set such options in your option list.

If you need more help, then we'll need more details: What kind of Cray
system is this? What options did you pass when you configured the
Einstein Toolkit? What output did you receive while configuring? etc.

-erik

On Mon, Aug 29, 2016 at 12:47 PM, L.S. Oswald  wrote:


Hello

I'm attempting to install the Einstein Toolkit on Dora, which is a
Cray
system supercomputer. In doing so I came across the following
error:

Configuration script for thorn MPI returned exit code 5
Error message: 'MPI could not be configured: neither
automatic nor
manual configuration succeeded'

In addition the log stated that:
No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR =
/usr)

I subsequently discovered that it was looking in the wrong place
for the
MPI root directory and that the reason it was looking under /usr
instead
of /opt/cray/mpt/7.3.2/gni/mpich-cray/8.3 was because that was the
setting in the ubuntu configuration file that I had used when
configuring SimFactory. On a reattempt therefore I did not use the
ubuntu.cfg file when configuring SimFactory, and got the following
error
instead:

Configuring with flesh MPI
Warning: use of flesh MPI via MPI option is deprecated and
should be replaced with the thorn ExternalLibraries/MPI and its
MPI_DIR
option
MPI selected, but no known MPI method - what is
"/opt/cray/mpt/7.3.2/gni/mpich-cray/8.3" ?

Attempts at altering the Makefile and the config-info file resulted
in
either no change, or more errors.

Please would you be able to advise me on the correct way to specify
the
root directory for MPI?

Many thanks,

Lucy Oswald
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Links:
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[1] http://lists.einsteintoolkit.org/mailman/listinfo/users
[2] http://www.perimeterinstitute.ca/personal/eschnetter/Using configuration: sim
Updated thorn list for configuration sim
Building sim
Cactus - version: 4.3.0
Building configuration sim
Reconfiguring thorns
Reading ThornList...
Parsing configuration files...
Parsing interface files...
   ADMAnalysis
   Implements: ADMAnalysis
   Inherits:   ADMBase  StaticConformal  Grid  ADMMacros
   6 Public, 0 Protected, 0 Private variable groups
   ADMBase
   Implements: ADMBase
   Inherits:   grid
   9 Public, 0 Protected, 0 Private variable groups
   ADMCoupling
   Implements: ADMCoupling
   0 Public, 0 Protected, 0 Private variable groups
   ADMMacros
   Implements: ADMMacros
   1 Public, 0 Protected, 0 Private variable groups
   ADMMass
   Implements: ADMMass
   Inherits:   ADMBase ADMMacros StaticConformal SpaceMask
   0 Public, 0 Protected, 6 Private variable groups
   AEILocalInterp
   Implements: AEILocalInterp
   0 Public, 0 Protected, 0 Private variable groups
   AHFinder
   Implements: AHFinder
   Inherits:   ADMBase StaticConformal SpaceMask Grid IO ADMMacros
   6 Public, 0 Protected, 10 Private variable groups
   AHFinderDirect
   Implements: AHFinderDirect
   Inherits:   Grid ADMBase StaticConformal SpaceMask SphericalSurface 
IO
   0 Public, 0 Protected, 5 Private variable groups
   BLAS
   Implements: BLAS
   0 Public, 0 Protected, 0 Private variable groups
   Boundary
   Implements: boundary
   0 Public, 0 Protected, 0 Private variable groups
   CT_Analytic
   Implements: CT_Analytic
   Inherits: Boundary GenericFD Grid
   40 Public, 0 Protected, 0 Private variable groups
   CT_MultiLevel
   Implements: CT_MultiLevel
   Inherits:   Boundary Grid
   0 Public, 0 Protected, 9 Private variable groups
   Cactus
   Implements: Cactus
   0 Public, 0 Protected, 0 Private variable groups
   CalcK
   Implements:

Re: [Users] Problem with compiling Einstein Toolkit on Cray system

2016-09-06 Thread L.S. Oswald 
Hi Rahul

Thanks very much for your help.

I hadn't tried that. I think I managed to partially solve the MPI issue 
by creating a new .cfg file specifying the path, but I have since come 
up against various other errors preventing me from compiling. I just 
tried including your line in the config-info file but no luck so far.

Consequently I've been trying to install the Toolkit on a different 
computer, and this one has gone much farther. It seems to compile 
everything and then stop at the end, so that it doesn't create the 
executable. This is the error I get:

/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: 
/home/ara/loswald/Cactus/configs/sim/lib/libthorn_SystemTopology.a(system_topology.cc.o):
 
undefined reference to symbol 'opal_hwloc172_hwloc_topology_get_support'
/usr/lib64/mpi/gcc/openmpi/lib64/libopen-pal.so.6: error adding symbols: 
DSO missing from command line
collect2: error: ld returned 1 exit status
/home/ara/loswald/Cactus/lib/make/make.configuration:149: recipe for 
target '/home/ara/loswald/Cactus/exe/cactus_sim' failed

I'm unclear on what hwloc actually is: is it a library in itself or 
should it be part of open-pal or MPI? Only one configuration file 
references hwloc specifically so we created a new configuration file 
which included the following lines:

# OpenMPI contains a copy of hwloc, use it
HWLOC_DIR = NO_BUILD
HWLOC_INC_DIRS = 
/usr/lib64/mpi/gcc/openmpi/include/openmpi/opal/mca/hwloc 
/usr/lib64/mpi/gcc/openmpi/include/openmpi/o
pal/mca/hwloc/hwloc172 
/usr/lib64/mpi/gcc/openmpi/include/openmpi/opal/mca/hwloc/hwloc172/hwloc/include
 
/usr/lib64/mpi/
gcc/openmpi/include/openmpi
HWLOC_LIBS =  -llibopen-pal

but this had no effect and I got the same error.

I don't suppose you could enlighten me on how I might go about adding 
the DSO to the command line, and indeed, what DSO I should be adding?

Many thanks,

Lucy

On 2016-09-06 4:27 pm, rahul kashyap wrote:
> Hi Lucy,
> 
> Did you try including this line in /configs/my_config/config-info
> 
> MPI_DIR=path/to/MPI/bin
> 
> then do make my_config
> 
> Best,
> rahul
> 
> On Mon, Aug 29, 2016 at 12:47 PM, L.S. Oswald  wrote:
> 
>> Hello
>> 
>> I'm attempting to install the Einstein Toolkit on Dora, which is a
>> Cray
>> system supercomputer. In doing so I came across the following
>> error:
>> 
>> Configuration script for thorn MPI returned exit code 5
>> Error message: 'MPI could not be configured: neither
>> automatic nor
>> manual configuration succeeded'
>> 
>> In addition the log stated that:
>> No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR =
>> /usr)
>> 
>> I subsequently discovered that it was looking in the wrong place
>> for the
>> MPI root directory and that the reason it was looking under /usr
>> instead
>> of /opt/cray/mpt/7.3.2/gni/mpich-cray/8.3 was because that was the
>> setting in the ubuntu configuration file that I had used when
>> configuring SimFactory. On a reattempt therefore I did not use the
>> ubuntu.cfg file when configuring SimFactory, and got the following
>> error
>> instead:
>> 
>> Configuring with flesh MPI
>> Warning: use of flesh MPI via MPI option is deprecated and
>> should be replaced with the thorn ExternalLibraries/MPI and its
>> MPI_DIR
>> option
>> MPI selected, but no known MPI method - what is
>> "/opt/cray/mpt/7.3.2/gni/mpich-cray/8.3" ?
>> 
>> Attempts at altering the Makefile and the config-info file resulted
>> in
>> either no change, or more errors.
>> 
>> Please would you be able to advise me on the correct way to specify
>> the
>> root directory for MPI?
>> 
>> Many thanks,
>> 
>> Lucy Oswald
>> ___
>> Users mailing list
>> Users@einsteintoolkit.org
>> http://lists.einsteintoolkit.org/mailman/listinfo/users [1]
> 
> 
> 
> Links:
> --
> [1] http://lists.einsteintoolkit.org/mailman/listinfo/users
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Re: [Users] Problem with compiling Einstein Toolkit on Cray system

2016-09-06 Thread Erik Schnetter 
Lucy

The Simulation Factory has several example option lists for Cray systems;
look e.g. at bluewaters or edison. I don't recommend changing the
"config-info" file, since this file will be overwritten. Instead, you can
set such options in your option list.

If you need more help, then we'll need more details: What kind of Cray
system is this? What options did you pass when you configured the Einstein
Toolkit? What output did you receive while configuring? etc.

-erik


On Mon, Aug 29, 2016 at 12:47 PM, L.S. Oswald  wrote:

> Hello
>
> I'm attempting to install the Einstein Toolkit on Dora, which is a Cray
> system supercomputer. In doing so I came across the following error:
>
>Configuration script for thorn MPI returned exit code 5
>Error message: 'MPI could not be configured: neither automatic nor
> manual configuration succeeded'
>
> In addition the log stated that:
>No MPI compiler wrapper found beneath MPI_DIR (MPI_DIR = /usr)
>
> I subsequently discovered that it was looking in the wrong place for the
> MPI root directory and that the reason it was looking under /usr instead
> of /opt/cray/mpt/7.3.2/gni/mpich-cray/8.3 was because that was the
> setting in the ubuntu configuration file that I had used when
> configuring SimFactory. On a reattempt therefore I did not use the
> ubuntu.cfg file when configuring SimFactory, and got the following error
> instead:
>
>Configuring with flesh MPI
>  Warning: use of flesh MPI via MPI option is deprecated and
> should be replaced with the thorn ExternalLibraries/MPI and its MPI_DIR
> option
>  MPI selected, but no known MPI method - what is
> "/opt/cray/mpt/7.3.2/gni/mpich-cray/8.3" ?
>
> Attempts at altering the Makefile and the config-info file resulted in
> either no change, or more errors.
>
> Please would you be able to advise me on the correct way to specify the
> root directory for MPI?
>
> Many thanks,
>
> Lucy Oswald
> ___
> Users mailing list
> Users@einsteintoolkit.org
> http://lists.einsteintoolkit.org/mailman/listinfo/users
>



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