intel gnu toolchain fails

[Ronald Cohen]

I am trying to use the intel gnu toolchain on my KNL cluster using GNU, and it always faiuls for every version of the intel suite I can find with the following:

make   ARCH=Linux-x86-64-intelx ELPAROOT=/home/rcohen/gnu/gcc6.3/  AVX=3 OMP=1 GNU=1 MKL=2 MIC=1 VERSION=psmp

to1: fatal error: multiple prevailing defs for ?libxsmm_gemm_auto_prefetch_default?

compilation terminated.

lto-wrapper: fatal error: gfortran returned 1 exit status

compilation terminated.

/usr/bin/ld: error: lto-wrapper failed

collect2: error: ld returned 1 exit status

/home/rcohen/CP2K/cp2k/obj/Linux-x86-64-intelx/psmp/all.dep:86: recipe for target '/home/rcohen/CP2K/cp2k/exe/Linux-x86-64-intelx/graph.psmp' failed

make[3]: *** [/home/rcohen/CP2K/cp2k/exe/Linux-x86-64-intelx/graph.psmp] Error 1

make[3]: *** Waiting for unfinished jobs....

I cannot find a fix for the "multiple prevaiing ..." or that anyone else has reported it. Any help is appreciated.

The gnu toolchain built find, but without elpa or mkl. I was trying to add in elpa and mkl.

Ron Cohen

[Mohammad Shakiba]

Dear Ronald,

I had problems with compiling CP2K with intel compilers too. I want to share my experience about compiling CP2K with intel. Some of them works properly and some not. The recommended versions are included in the following links:

https://www.cp2k.org/dev:compiler_support

https://xconfigure.readthedocs.io/en/latest/cp2k/

Use the links above which are good for compiling locally on clusters. First, you're gonna have to recompile libxsmm yourself in the $HOME directory (use the link in xconfigure and the rest). Then based on your CPU (type 'lscpu' to find out what kind of cpu you got, for example I have Xeon-E5-v4) you have to source to the intel compiler:

source /opt/intel/compilers_and_libraries_yourversion/linux/bin/compilervas.sh intel64

Always source to intel compiler like above before using CP2K. You can check that by typing for example 'mpirun --version'. Also, check if your CP2K version pass the regtests, for example it compiles with intel 17.0.1 but with wrong answers.

Hope you find it useful.

[Ron Cohen]

Thank you, but to be clear I am using gnu compilers, as called by the intel distribution, using the intel tool chain with GNU=1. I am properly sourcing the intel variable scripts and the correct compilers are being used. Still I get the reported error. Thanks,

Ron 

Sent from my iPhone

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[Ronald Cohen]

I got the code to build with the following change to the arch file:

    ifneq (0,$(IPO))
      OPTFLAGS += -flto -Wl,-flto -Wno-lto-type-mismatch
    else
      OPTFLAGS += -fno-lto -Wl,-fno-lto -Wno-lto-type-mismatch
    endif

However, now a new problem, with gcc6.3 and with 8.2 and 8.3:

  /   \                                                                      *
 * [ABORT]                                                                     *
 *  \___/                        Thread number has changed                     *
 *    |                                                                        *
 *  O/|                                                                        *
 * /| |                                                                        *
 * / \                                                dbcsr_dist_methods.F:519 *
 *******************************************************************************


 ===== Routine Calling Stack =====

           10 dbcsr_create_new
            9 build_overlap_matrix
            8 build_core_hamiltonian_matrix
            7 qs_energies_init_hamiltonians
            6 qs_energies
            5 qs_forces
            4 cp_eval_at
            3 geoopt_bfgs
            2 cp_geo_opt
            1 CP2K

For some reason it works tith the gnu toolchainj but always have this problem with gnu compilers but intel toolchain.

It seems like OMP_GET_NUM_THREADS()

always reports 1 thread though there are 4.

Ron

On Monday, April 8, 2019 at 5:38:41 PM UTC-4, Ronald Cohen wrote:

Thank you, but to be clear I am using gnu compilers, as called by the intel distribution, using the intel tool chain with GNU=1. I am properly sourcing the intel variable scripts and the correct compilers are being used. Still I get the reported error. Thanks,

Ron 

Sent from my iPhone

[Hans Pabst]

This issue occassionally happens depending on the toolchain. It may have something to do with the version of Bintools. The problem can be avoided with adding IPO=0 to the make-command (no edit of the Make/Arch file needed).

[Ronald Cohen]

Thank you! How can binutils effect this? Ron

---
Ron Cohen
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skypename: ronaldcohen

twitter: @recohen3

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[Hans Pabst]

In addition, the latest ARCH files avoid this problem even if IPO/LTO is enabled. Please note that LTO is enabled by default when using the GNU toolchain. Apparently, LTO is not as exercised as the regular build/link flow and there are occassionally issues related to LTO when building complex applications.