[Users] error message MPI
Hamilton, Maria
babiuc at marshall.edu
Tue Oct 9 13:07:56 CDT 2018
Hello Steve,
I tried again to compile cactus on osx, in fact I erase the whole cactus, did a fresh download of the current development version, brew reinstalled gcc-8 --without-multilib and brew reinstall openmpi --build-from-source --cc=gcc-8, then did a ./simfactory/bin/sim setup-silent --optionlist=osx-homebrew.cfg --runscript generic-mpi.run and ./simfactory/bin/sim build.
The good news is that I don't have any more complains about LORENE and PAPI.
The bad news is that I have the same errors in dh.cc
COMPILING arrangements/Carpet/CarpetLib/src/dh.cc
/Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)':
/Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23 error: 'MPI_UB' was not declared in this scope
{1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
^~~~~~
/Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23 note: suggested alternative: 'MPI_IO'
{1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
^~~~~~
MPI_IO
/Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::fast_dboxes&)':
/Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23 error: 'MPI_UB' was not declared in this scope
{1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
^~~~~~
/Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23 note: suggested alternative: 'MPI_IO'
{1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
^~~~~~
MPI_IO
make[3]: *** [dh.cc.o] Error 1
Maria
_______________________
Dr. Maria C. Babiuc Hamilton
Department of Physics
Marshall University
S257 Science Building
Huntington, WV, 25755
Phone: (304)696-2754
________________________________________
From: users-bounces at einsteintoolkit.org <users-bounces at einsteintoolkit.org> on behalf of Steven R. Brandt <sbrandt at cct.lsu.edu>
Sent: Thursday, October 4, 2018 1:21 PM
To: users at einsteintoolkit.org
Subject: Re: [Users] error message MPI
I recently pushed a change for osx. If you redo your setup (i.e. remove
etc/defs.local.ini and mdb/machines/your-machine.ini) and try again, it
may help.
Is mpicxx in your command path? I.e. if you type 'which mpicxx' do you
see anything?
Thanks.
--Steve
On 10/04/2018 08:43 AM, Hamilton, Maria wrote:
> Roland,
>
> A quick update. My hacking managed to get the code compiled, but it hangs on when running. I'm sure I did something wrong.
> I'll wait for your pointers after you have time to install and run Cactus on Mojave.
>
> Maria
>
> _______________________
> Dr. Maria C. Babiuc Hamilton
> Department of Physics
> Marshall University
> S257 Science Building
> Huntington, WV, 25755
> Phone: (304)696-2754
>
>
> ________________________________________
> From: users-bounces at einsteintoolkit.org <users-bounces at einsteintoolkit.org> on behalf of Hamilton, Maria <babiuc at marshall.edu>
> Sent: Wednesday, October 3, 2018 10:52 PM
> To: rhaas at illinois.edu
> Cc: users at einsteintoolkit.org
> Subject: Re: [Users] error message MPI
>
> Roland,
>
> OK, keep me updated. Honestly, I am afraid to update to Mojave!
>
> I do wander why Cactus consistently breaks down after any new updates I do on my mac laptop. Is it because of home-brew?
> Or shall I just stick with older versions of the software libraries?
> It finally compiled, after I commented out LORENE, PAPI, and the Meudon thorns, and did some hacking in the CarpetLib thorn.
> Clearly, my new brew update made MPU_UB deprecated.
> I ended up defining MPI-UB everywhere it was needed as:
> #define MPI_UB ((MPI_Datatype)16)
> This should have been in an mpi.h file, but apparently is not.
> It also complained about MPI_Type_struct, which I commented out.
>
> I have an older Ubuntu workstation, and the new Cactus compiled there without any problems.
>
> I reinstalled also the new Cactus on BigGreen, the cluster at Marshall University, and it went well.
>
> One last thing: I could not find any ubuntu.cfg.
> Also, I don't see a cents.cfg either.
> Any suggestion about what to use instead?
> I would like to have some flexibility on what version of compilers to use.
>
> cheers,
> Maria
>
> _______________________
> Dr. Maria C. Babiuc Hamilton
> Department of Physics
> Marshall University
> S257 Science Building
> Huntington, WV, 25755
> Phone: (304)696-2754
>
>
> ________________________________________
> From: Roland Haas <rhaas at illinois.edu>
> Sent: Wednesday, October 3, 2018 10:20 AM
> To: Hamilton, Maria
> Cc: users at einsteintoolkit.org
> Subject: Re: [Users] error message MPI
>
> Hello Maria,
>
> this will take a while. Installing Mojave is complicated for me and I
> likely will not get to it until at least after Oct 15th, sorry.
>
> Yours,
> Roland
>
>> Hello Roland,
>>
>> OK, thanks! It would be great if you let me know how the compilation went on your new mac.
>> The errors I had were popping out at Carpet/CarpetLib/src/dh.cc were for the compilation from scratch.
>>
>> I did try to use sim as well, as you suggested, and I had a cascade of errors.
>> The first complaint was about LORENE:
>> _______________
>> LORENE: Installing...
>> ~/Cactus/configs/sim/scratch
>> LORENE: Cleaning up...
>> LORENE: Done.
>> Creating /Users/babiuc/Cactus/configs/sim/lib/libthorn_LORENE.a
>> make: *** [sim] Error 2
>> __________
>>
>>
>> I commented LORENE out and I had to comment out 3 more thorns:
>> CST error 1:
>> -> Thorn 'Meudon_Bin_BH' requires the capability 'LORENE'.
>> Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Bin_BH' from it !
>>
>>
>> CST error 2:
>> -> Thorn 'Meudon_Bin_NS' requires the capability 'LORENE'.
>> Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Bin_NS' from it !
>>
>>
>> CST error 3:
>> -> Thorn 'Meudon_Mag_NS' requires the capability 'LORENE'.
>> Please add a thorn that provides 'LORENE' to your ThornList or remove 'Meudon_Mag_NS' from it !
>>
>>
>> Then I had an error at thorn PAPI:
>> _______
>> Checking status of thorn PAPI
>> PAPI: Preparing directory structure...
>> PAPI: Unpacking archive...
>> ~/Cactus/configs/sim/scratch/build/PAPI ~/Cactus/configs/sim/scratch
>> PAPI: Applying patches...
>> ~/Cactus/configs/sim/scratch/build/PAPI/papi-5.3.0 ~/Cactus/configs/sim/scratch/build/PAPI ~/Cactus/configs/sim/scratch
>> Cannot complete in-place edit of ./src/libpfm-3.y/examples_v2.x/ia64/mont_opcode.c: failed to rename work file './src/libpfm-3.y/examples_v2.x/ia64/XXxgZzZf' to './src/libpfm-3.y/examples_v2.x/ia64/mont_opcode.c': Bad file descriptor, <> line 32848.
>> make[2]: *** [make.checked] Error 2
>> make[1]: *** [/Users/babiuc/Cactus/configs/sim/lib/libthorn_PAPI.a] Error 2
>> make[1]: *** Waiting for unfinished jobs....
>> Creating /Users/babiuc/Cactus/configs/sim/lib/libthorn_LocalReduce.a
>> make: *** [sim] Error 2
>> ___________________
>>
>> In the end I arrived at the same error:
>>
>> ____
>> COMPILING arrangements/Carpet/CarpetLib/src/dh.cc
>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)':
>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: error: 'MPI_UB' was not declared in this scope
>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>> ^~~~~~
>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: note: suggested alternative: 'MPI_IO'
>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>> ^~~~~~
>> MPI_IO
>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::fast_dboxes&)':
>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: error: 'MPI_UB' was not declared in this scope
>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>> ^~~~~~
>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: note: suggested alternative: 'MPI_IO'
>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>> ^~~~~~
>> MPI_IO
>> make[3]: *** [dh.cc.o] Error 1
>> _____________
>>
>>
>> Also, a thorn seems to be empty:
>> Missing thorn EinsteinInitialData/Hydro_RNSID
>>
>>
>>
>> Maria
>>
>> _______________________
>> Dr. Maria C. Babiuc Hamilton
>> Department of Physics
>> Marshall University
>> S257 Science Building
>> Huntington, WV, 25755
>> Phone: (304)696-2754
>>
>>
>> ________________________________________
>> From: Roland Haas <rhaas at illinois.edu>
>> Sent: Tuesday, October 2, 2018 9:01 AM
>> To: Hamilton, Maria
>> Cc: users at einsteintoolkit.org
>> Subject: Re: [Users] error message MPI
>>
>> Hello Maria,
>>
>> please try compiling from scratch. Ie do
>>
>> make sim-realclean (or even rm -rf configs/sim)
>>
>> and try compiling again. It is possible that a previous abortive
>> attempt to compile has created a file "mpi.h" in your Cactus tree and
>> that this file is messing up things now.
>>
>> If you already did start from scratch then I do not quite know what may
>> be going on (I do not normally use a Mac).
>>
>> I am updating my own mac today and will see if I get similar results.
>>
>> Yours,
>> Roland
>>
>>> Hello Roland,
>>>
>>> It turned out that I still have problems with MPI.
>>> I did not update to mojave, just did a brew update/brew upgrade.
>>> A smaller executable compiled fine, but compiling with most thorns activated, I have the following error:
>>>
>>> _____________________
>>> COMPILING arrangements/Carpet/CarpetLib/src/dh.cc
>>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::light_dboxes&)':
>>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: error: 'MPI_UB' was not declared in this scope
>>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>>> ^~~~~~
>>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2278:23: note: suggested alternative: 'MPI_IO'
>>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>>> ^~~~~~
>>> MPI_IO
>>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc: In function 'ompi_datatype_t* mpi_datatype(const dh::fast_dboxes&)':
>>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: error: 'MPI_UB' was not declared in this scope
>>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>>> ^~~~~~
>>> /Users/babiuc/Cactus/arrangements/Carpet/CarpetLib/src/dh.cc:2330:23: note: suggested alternative: 'MPI_IO'
>>> {1, sizeof s, MPI_UB, "MPI_UB", "MPI_UB"}};
>>> ^~~~~~
>>> MPI_IO
>>> ___________________
>>>
>>> My mpic++ does not take -compile_info, but a show gives me this:
>>>
>>> $ mpic++ --showme
>>> clang++ -I/usr/local/Cellar/open-mpi/HEAD-73075b8/include -L/usr/local/opt/libevent/lib -L/usr/local/Cellar/open-mpi/HEAD-73075b8/lib -lmpi
>>>
>>> What do you suggest?
>>>
>>> thanks,
>>> Maria
>>>
>>> _______________________
>>> Dr. Maria C. Babiuc Hamilton
>>> Department of Physics
>>> Marshall University
>>> S257 Science Building
>>> Huntington, WV, 25755
>>> Phone: (304)696-2754
>>>
>>>
>>> ________________________________________
>>> From: Roland Haas <rhaas at illinois.edu>
>>> Sent: Monday, October 1, 2018 4:59 PM
>>> To: Hamilton, Maria
>>> Cc: users at einsteintoolkit.org
>>> Subject: Re: [Users] error message MPI
>>>
>>> Hello Maria,
>>>
>>> if by update you mean an update of the OS (to Mojave) or the package
>>> manager (Homebrew, Macports) then most likely the update made you MPI
>>> stack unusable.
>>>
>>> I would try the following:
>>>
>>> 1. if you updated the OS to Mojave then quite likely you will have to
>>> reinstall the package manager and all packages
>>> (https://apple.stackexchange.com/questions/85480/how-should-i-fix-my-homebrew-installation-after-upgrading-os-x)
>>> though if you are lucky a "brew upgrade" may do the trick
>>>
>>> 2. check the output of the commands the Cactus tried ie:
>>> usr/local/bin/mpic++ -compile_info and /usr/local/bin/mpic++ --showme
>>> to see what kind of error is produced. Likely you have to re-install
>>> the MPI package from your package manager (same as point 1. really).
>>>
>>> Yours,
>>> Roland
>>>
>>>> Hello,
>>>>
>>>>
>>>> I'm trying to compile the development Cactus version on my Mac laptop
>>>> after an update:
>>>>
>>>> $repos/CRL/GetComponents --update.
>>>>
>>>> Unfortunately, I ran into the following error:
>>>>
>>>> ********************************************************************************
>>>>
>>>> Running configuration script for thorn MPI:
>>>>
>>>> Found MPI compiler wrapper at /usr/local/bin/mpic++!
>>>>
>>>> sh: line 1: 30205 Abort trap: 6 /usr/local/bin/mpic++
>>>> -compile_info 2> /dev/null
>>>>
>>>> sh: line 1: 30207 Abort trap: 6 /usr/local/bin/mpic++
>>>> --showme 2> /dev/null
>>>>
>>>> ERROR: MPI could not be configured: neither automatic nor manual
>>>> configuration succeeded
>>>>
>>>>
>>>> CST error 1:
>>>>
>>>> -> Configuration script for thorn MPI returned exit code 5
>>>>
>>>> Error message: 'MPI could not be configured: neither automatic
>>>> nor manual configuration succeeded'
>>>>
>>>>
>>>> Finished running configuration script for thorn MPI.
>>>>
>>>>
>>>> ********************************************************************************
>>>>
>>>> This persists after real clean, and even after I erase the
>>>> configuration and reconfigure it.
>>>>
>>>> Please help,
>>>> Maria
>>>> ?
>>>>
>>>>
>>>> _______________________
>>>> Dr. Maria C. Babiuc Hamilton
>>>> Department of Physics
>>>> Marshall University
>>>> S257 Science Building
>>>> Huntington, WV, 25755
>>>> Phone: (304)696-2754
>>>>
>>>
>>>
>>> --
>>> My email is as private as my paper mail. I therefore support encrypting
>>> and signing email messages. Get my PGP key from http://pgp.mit.edu .
>>
>> --
>> My email is as private as my paper mail. I therefore support encrypting
>> and signing email messages. Get my PGP key from http://pgp.mit.edu .
>
> --
> My email is as private as my paper mail. I therefore support encrypting
> and signing email messages. Get my PGP key from http://pgp.mit.edu .
> _______________________________________________
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