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
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...) 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 automaticnor 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
That was it! After reinstalling open-mpi with brew upgrade, it worked!
Thank you, 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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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...) 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 automaticnor 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 .
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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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...) 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 automaticnor 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 .
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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 .
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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 .
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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 .
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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 .
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Steven R. Brandt sbrandt@cct.lsu.edu Sent: Thursday, October 4, 2018 1:21 PM To: users@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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
_______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hello Maria,
would you mind trying the following:
cd repos/carpet git cherry-pick 5073af2c
then try and compile?
This commit is part of the proposed updated to Carpet that Steve is currently reviewing and that we will commit in short order.
Yours, Roland
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Steven R. Brandt sbrandt@cct.lsu.edu Sent: Thursday, October 4, 2018 1:21 PM To: users@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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
That actually worked! The only complaint I had was at PAPI, but after I disabled it, the compilation went all the way to the end.
Thank you! 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@illinois.edu Sent: Tuesday, October 9, 2018 2:28 PM To: Hamilton, Maria Cc: Steven R. Brandt; users@einsteintoolkit.org Subject: Re: [Users] error message MPI
Hello Maria,
would you mind trying the following:
cd repos/carpet git cherry-pick 5073af2c
then try and compile?
This commit is part of the proposed updated to Carpet that Steve is currently reviewing and that we will commit in short order.
Yours, Roland
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Steven R. Brandt sbrandt@cct.lsu.edu Sent: Thursday, October 4, 2018 1:21 PM To: users@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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
-- 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 .
Hello Maria,
the commit that you cherry picked is now in master and this should be fine in the future.
Yours, Roland
That actually worked! The only complaint I had was at PAPI, but after I disabled it, the compilation went all the way to the end.
Thank you! 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@illinois.edu Sent: Tuesday, October 9, 2018 2:28 PM To: Hamilton, Maria Cc: Steven R. Brandt; users@einsteintoolkit.org Subject: Re: [Users] error message MPI
Hello Maria,
would you mind trying the following:
cd repos/carpet git cherry-pick 5073af2c
then try and compile?
This commit is part of the proposed updated to Carpet that Steve is currently reviewing and that we will commit in short order.
Yours, Roland
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Steven R. Brandt sbrandt@cct.lsu.edu Sent: Thursday, October 4, 2018 1:21 PM To: users@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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
-- 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 .
This constant is supposed to exist in MPI.
Do you have mpicxx in your path? I.e. what do you see when you type "which mpicxx"?
If it's there, what do you get when you type "mpicxx --version"?
--Steve
On 10/09/2018 01:07 PM, Hamilton, Maria wrote:
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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Steven R. Brandt sbrandt@cct.lsu.edu Sent: Thursday, October 4, 2018 1:21 PM To: users@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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 .
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Note, there should not be special configs for different os flavors anymore, no debian.cfg or ubuntu.cfg.
--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@einsteintoolkit.org users-bounces@einsteintoolkit.org on behalf of Hamilton, Maria babiuc@marshall.edu Sent: Wednesday, October 3, 2018 10:52 PM To: rhaas@illinois.edu Cc: users@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@illinois.edu Sent: Wednesday, October 3, 2018 10:20 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Tuesday, October 2, 2018 9:01 AM To: Hamilton, Maria Cc: users@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@illinois.edu Sent: Monday, October 1, 2018 4:59 PM To: Hamilton, Maria Cc: users@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:
- 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...) though if you are lucky a "brew upgrade" may do the trick
- 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 automaticnor 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 . _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hello Maria,
OK, keep me updated. Honestly, I am afraid to update to Mojave!
It is the same procedure as every OSX update. Everything breaks :-)
I do wander why Cactus consistently breaks down after any new updates I do on my mac laptop. Is it because of home-brew?
I would point me finger at homebrew, yes. The only real way to safely deal with OS updates in homebrew seems to wipe all of homebrew and reinstall it from scratch. Cactus itself likely works fine with it once it is properly installed.
Or shall I just stick with older versions of the software libraries?
The issue seems to be that some of homebrew relies on OSX system libraries. Those libraries all got updated when the OS update and now the programs in homebrew (which were not update) no longer work.
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
That could be the case yes. The very newest version of Carpet to be put into the development branch (master) on Monday seems to remove references to MPI_UB which may need to be backported into the release branch if this is indeed creating issues.
One last thing: I could not find any ubuntu.cfg.
In master it was removed on Monday and I think Steve already responded in a separate email pointing out that it should no longer be required and one can use generic.cfg instead. It should still be present in the release branch ET_2018_09 though. Are you using the release branch or the master (development) branch?
Also, I don't see a cents.cfg either. Any suggestion about what to use instead?
Steve's email should address both of these.
I would like to have some flexibility on what version of compilers to use.
You would have to create one cfg file per compiler version to use and either specify it by hand to simfactory when building ie. simfactory/bin/sim build --optionlist myoptions-gcc7.cfg or make up a machine.ini file per compiler version and use that (using the --machine option) or (this may be simplest) add a "optionlist" entry to your machine's "[<machine>]" section in simfactory/etc/defs.local.ini specifying the configuration file you would like to use.
Yours, Roland
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Hamilton, Maria -
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Steven R. Brandt