Problems compiling v.1.2.3 on 32bit Scientific linux with gcc

OpenKIM
1

Our linux cluster is running 32 bit Scientific Linux.
When I try to compile v1.2.3 of the API it starts well, but then make fails.
I’ve attached the output below.
It may or may not be relevant that adding -lgfortranstart to LDFLAGS ( as suggested in the install instructions ) throws a link error
/usr/bin/ld: cannot find -lgfortranstart
at the end of make examples, so I have removed that library from the following.

Any help appreciated,

Daniel

[dmason@fuslw111 openkim-api-v1.2.3]$ cat /proc/version
Linux version 2.6.32-431.1.2.el6.i686 ([email protected]) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC) ) #1 SMP Thu Dec 12 13:59:21 CST 2013

[dmason@fuslw111 openkim-api-v1.2.3]$ gcc -v
Using built-in specs.
Target: i686-redhat-linux
Configured with: …/configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre --enable-libgcj-multifile --enable-java-maintainer-mode --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --disable-libjava-multilib --with-ppl --with-cloog --with-tune=generic --with-arch=i686 --build=i686-redhat-linux
Thread model: posix
gcc version 4.4.6 20120305 (Red Hat 4.4.6-4) (GCC)

[dmason@fuslw111 openkim-api-v1.2.3]$ grep “LDFLAGS” Makefile.KIM_Config
LDFLAGS = -lgfortran

[dmason@fuslw111 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 /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODEL_DRIVERS
  • installing… ex_model_driver_P_Morse … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODEL_DRIVERS
  • installing… ex_model_driver_P_LJ … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODEL_DRIVERS
  • installing… ex_model_Ar_P_MLJ_NEIGH_RVEC_F … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_LJ … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_MLJ_C … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ne_P_MLJ_NEIGH_RVEC_H … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… EXAMPLES.README … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_MLJ_F90 … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ne_P_fastLJ … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_MLJ_CLUSTER_C … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_MLJ_NEIGH_PURE_H_F … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Al_PF_ErcolessiAdams … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_Morse … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ne_P_LJ_NEIGH_PURE_H … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_ArNe_P_MLJ_NEIGH_RVEC_F … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ne_P_LJ … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Cu_PF_Johnson … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_MLJ_CLUSTER_F90 … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ar_P_MLJ_MI_OPBC_H_F … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_model_Ne_P_Morse … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/MODELS
  • installing… ex_test_Ar_free_cluster_CLUSTER_C … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_free_cluster_CLUSTER_memory_F90 … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_FCCcohesiveCutoff_NEIGH_RVEC … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_multiple_models … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_ArNe_B2cohesive_NEIGH_RVEC … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ne_free_cluster … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ne_free_cluster_stiff … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ne_free_cluster_SI … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… EXAMPLES.README … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… run_forces_numer_deriv_for_all_models … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_free_cluster … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_free_cluster_CLUSTER_F90 … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… vc_forces_delta … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Al_free_cluster … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_FCCcohesive_NEIGH_RVEC … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… vc_forces_numer_deriv … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_FCCcohesive_NEIGH_PURE … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Al_FCCcohesive_MI_OPBC … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… vc_config_ener_forces … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Cu_free_cluster … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… ex_test_Ar_FCCcohesive_MI_OPBC … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS
  • installing… run_all_ex_tests … copied to /home/dmason/Programs/KIM/openkim-api-v1.2.3/TESTS

[dmason@fuslw111 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,

OK. I've managed to create a virtualbox version of scientific linux 6.5.
I don't, however, reproduce this problem...

The error is some sort of make error. Can you verify that you are using verson 3.82 of gnu make?

Ryan

3

Hi,

No, not 3.82, we only have 3.81 here.

[dmason@fuslw107 ~]$ make -v
GNU Make 3.81
Copyright © 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.

This program built for i386-redhat-linux-gnu

Daniel

4

OK! I think I can tell you how to fix this. Please perform the following commands to edit the file openkim-api-v1.2.3/Makefile

cd openkim\-api\-v1\.2\.3 sed -i 'bak' -e 's|\.\\ |\.@|g' Makefile

I believe this will allow the build to run and complete.

This fix (actually a somewhat better, but more complicated one) will be in the next release of the openkim-api package...

Cheers,

Ryan

5

This seems to make a lot of progress!
If I use
sed -i.bak -e 's|\.\\ |.@%|g’ Makefile

(note slight difference)

I get down to

[dmason@fuslw107 openkim-api-v1.2.3]$ make

6

Great! OK, I think I know how to fix this too!

Instead of:

LDFLAGS = -lgfortran -lgfortranbegin

try

LD = $(FC)
LDFLAGS = -lstdc++

See if that works....

Ryan

7

This seems to have done the trick. I’ve run the example in TESTS and get
% echo “ex_model_Ar_P_MLJ_CLUSTER_C” | ./ex_test_Ar_free_cluster_CLUSTER_F90
Please enter a valid KIM model name:

8

Great!!!! It was my pleasure. I'm glad we worked it out!

Cheers,

Ryan