Problems compiling v.1.2.3 on 64 bit Cygwin, gcc 4.8.1

OpenKIM
1

I would like to compile the openKIM API v.1.2.3 on my local desktop machine, which has a tried-and-tested 64 bit Cygwin environment.

Following the install instructions starts well, throws a few warnings, then fails with “undefined reference” errors. Full output below.

Any help to resolve this issue gratefully received,

Daniel

dmason@F6773 /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3

$make examples

Makefile:42: Makefile.ModelsList: No such file or directory

Makefile:42: Makefile.ModelDriversList: No such file or directory

Makefile:42: Makefile.TestsList: No such file or directory

Creating… Makefile.TestsList.

Creating… Makefile.ModelDriversList.

Creating… Makefile.ModelsList.

Creating… KIM_Config file… KIM_API/Makefile.KIM_Config.

Creating… KIM_Config file… MODEL_DRIVERS/Makefile.KIM_Config.

Creating… KIM_Config file… MODELS/Makefile.KIM_Config.

Creating… KIM_Config file… TESTS/Makefile.KIM_Config.

  • installing… EXAMPLES.README … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODEL_DRIVERS

  • installing… ex_model_driver_P_LJ … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODEL_DRIVERS

  • installing… ex_model_driver_P_Morse … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODEL_DRIVERS

  • installing… EXAMPLES.README … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Al_PF_ErcolessiAdams … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_ArNe_P_MLJ_NEIGH_RVEC_F … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_LJ … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_C … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_CLUSTER_C … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_CLUSTER_F90 … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_F90 … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_MI_OPBC_H_F … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_NEIGH_PURE_H_F … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_MLJ_NEIGH_RVEC_F … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ar_P_Morse … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Cu_PF_Johnson … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ne_P_fastLJ … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ne_P_LJ … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ne_P_LJ_NEIGH_PURE_H … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ne_P_MLJ_NEIGH_RVEC_H … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… ex_model_Ne_P_Morse … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS

  • installing… EXAMPLES.README … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Al_FCCcohesive_MI_OPBC … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Al_free_cluster … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_ArNe_B2cohesive_NEIGH_RVEC … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_FCCcohesiveCutoff_NEIGH_RVEC … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_FCCcohesive_MI_OPBC … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_FCCcohesive_NEIGH_PURE … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_FCCcohesive_NEIGH_RVEC … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_free_cluster … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_free_cluster_CLUSTER_C … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_free_cluster_CLUSTER_F90 … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_free_cluster_CLUSTER_memory_F90 … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ar_multiple_models … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Cu_free_cluster … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ne_free_cluster … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ne_free_cluster_SI … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… ex_test_Ne_free_cluster_stiff … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… run_all_ex_tests … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… run_forces_numer_deriv_for_all_models … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… vc_config_ener_forces … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… vc_forces_delta … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

  • installing… vc_forces_numer_deriv … copied to /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

dmason@F6773 /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3

$make

Creating… Makefile.TestsList.

Creating… Makefile.ModelDriversList.

Creating… Makefile.ModelsList.

Creating… KIM_Config file… KIM_API/Makefile.KIM_Config.

Creating… KIM_Config file… MODEL_DRIVERS/Makefile.KIM_Config.

Creating… KIM_Config file… MODELS/Makefile.KIM_Config.

Creating… KIM_Config file… TESTS/Makefile.KIM_Config.

2

Hi Daniel,

Can you check the following:

1) is there a KIM_API_DIRS.o file in the KIM_API directory?

2) what does the line containing the string "directoryPath" look like from the output of the command

% nm libkim.so

3) what is the output of the command

cd KIM\_API mane -n libkim.so

Thanks,

Ryan

3

Hi Ryan,

$cd KIM/openkim-api-v1.2.3/KIM_API

dmason@F6773 /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3/KIM_API
$ls
grep KIM_API_C.cpp KIM_API_DIRS.o KIM_AUX.h Makefile openkim-api-descriptor-file-match.o Unit_Handling.h
KIM_API.cpp KIM_API_C.h KIM_API_F.F90 KIM_AUX.o Makefile.KIM_Config README Unit_Handling.o
KIM_API.h KIM_API_C.o KIM_API_F.o kim_kinds.mod nm_libkim.so standard.kim
kim_api.mod KIM_API_Description.txt KIM_API_status.h libkim.a openkim-api-descriptor-file-match.cpp standard_kim_str.o
KIM_API.o KIM_API_DIRS.h KIM_AUX.cpp libkim.so openkim-api-descriptor-file-match.exe Unit_Handling.cpp

$nm libkim.so | grep “directoryPath”
000000059636bb30 T _Z13directoryPath17DirectoryPathTypePSt4listISsSaISsEE

$mane -n libkim.so
-bash: mane: command not found

*** OK, I don’t recognise this command either. Try this? ***

$make -n libkim.so
make: `libkim.so’ is up to date.

Thanks,

Daniel

I would like to compile the openKIM API v.1.2.3 on my local desktop
machine, which has a tried-and-tested 64 bit Cygwin environment.

Following the install instructions starts well, throws a few warnings, then
fails with “undefined reference” errors. Full output below.

Any help to resolve this issue gratefully received,

Daniel

dmason@F6773 /cygdrive/c/Users/dmason/Programs/KIM/openkim-api-v1.2.3

$make examples

Makefile:42: Makefile.ModelsList: No such file or directory

SEE ORIGINAL POST

4

OK, I think I've resolved the issue. I've just released openkim-api-v1.3.1 which I believe will work nicely for you now.

Please try v1.3.1 and let me know if your problem is resolved.

Cheers,

Ryan