compile problem #121

lpham01 · 2022-12-27T02:21:06Z

lpham01
Dec 27, 2022

Dear Dr. Tadano

I currently get the error message "Illegal instruction (core dumped)" for anphon binary when I install the latest version of alamode, but alm seems to work well.
Is this a common problem due to the updated version? If not, do you have any idea how to solve the problem?

I really appreciate any help you can provide.

ttadano · 2022-12-27T02:25:47Z

ttadano
Dec 27, 2022
Maintainer

Could you explain in more detail how I can reproduce the problem?

6 replies

ttadano Dec 27, 2022
Maintainer

Unfortunately, that information alone is inadequate for reproducing the error because the compilers and libraries linked by CMake are system dependent.

I would suggest testing the conda install instead of using the native environment first and seeing if the error still exists.

lpham01 Dec 27, 2022
Author

This is the error message that I got when I install using conda environment.

ttadano Dec 28, 2022
Maintainer

I could successfully install the latest version using the following procedure without the reported issue.

conda create -n alamode -c conda-forge python=3
conda activate alamode
conda install -c conda-forge compilers openmpi boost eigen cmake spglib fftw scipy numpy h5py ipython
git clone https://github.com/ttadano/alamode.git
cd alamode
mkdir _build; cd _build
cmake ..
make -j

I've tested with various environments, including M1 Mac, intel Mac, CentOS, and Ubuntsu. In all cases, the installation was successful.

LePingKYXK Jul 17, 2023

Dear Dr. Tadano,
I succeed in installation following the instruction of https://alamode.readthedocs.io/en/latest/install.html#install-using-conda-recommended-for-non-experts. However, the Note at the end of section 3.2 made me confused.

when using the binaries, it may be necessary to set $LD_LIBRARY_PATH as**

% export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$CONDA_PREFIX/lib64:$LD_LIBRARY_PATH

Does it seem that I only need to add the conda virtual environment into the ~/.bashrc, not the PTAH of ALM or ANPHON?

ttadano Sep 20, 2023
Maintainer

Did you see any errors related to the dynamic libraries? For example, did alm command work? If so, you don't need to set LD_LIBRARY_PATH as suggested above.

ALukmantoro16 · 2023-09-18T08:27:04Z

ALukmantoro16
Sep 18, 2023

Dear @lpham01 @LePingKYXK @ttadano

Hii, I got same problem when i run the last step of phonon dispersion using anphon compiler. In my environment, I use ubuntu 20.04 and intel compiler. I've installed alamode following the instruction in https://alamode.readthedocs.io/en/latest/install.html#install-using-conda-recommended-for-non-experts .

Do you have any idea to overcome this error?
Thanks

This is the error message that I got when I install using conda environment.

1 reply

ttadano Sep 20, 2023
Maintainer

I followed the instructions on the documentation page with Ubuntu 18.04 and found no issues.

If you used the develop branch of alamode, can you try again with an older version (v.1.4.2)?

16-vikrant · 2024-02-13T18:10:27Z

16-vikrant
Feb 13, 2024

Dear @ALukmantoro16 @ttadano @LePingKYXK @lpham01

I am also facing a similar error while running the PbTe example on a supercomputer. Also, I tried installing ALAMODE on the Ubuntu 18 workstation. conda install -c conda-forge failed every time during the environment solving.

Can you help me with these issues?

Thank you!

9 replies

16-vikrant Feb 14, 2024

I got this output

(alamode) kandpal@ws158:~$ ldd alamode/_build/anphon/anphon
        linux-vdso.so.1 (0x00007ffeaccfb000)
        libmkl_intel_lp64.so.2 => /opt/intel/oneapi/mkl/2023.2.0/lib/intel64/libmkl_intel_lp64.so.2 (0x00001479d883a000)
        libmkl_intel_thread.so.2 => /opt/intel/oneapi/mkl/2023.2.0/lib/intel64/libmkl_intel_thread.so.2 (0x00001479d520e000)
        libmkl_core.so.2 => /opt/intel/oneapi/mkl/2023.2.0/lib/intel64/libmkl_core.so.2 (0x00001479d0e96000)
        libiomp5.so => /opt/intel/oneapi/compiler/2023.2.1/linux/compiler/lib/intel64_lin/libiomp5.so (0x00001479d0a54000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00001479d06b6000)
        libmpi.so.40 => /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so.40 (0x00001479d053f000)
        libstdc++.so.6 => /home/kandpal/bin/anaconda3/envs/alamode/lib/libstdc++.so.6 (0x00001479d035c000)
        libgcc_s.so.1 => /home/kandpal/bin/anaconda3/envs/alamode/lib/libgcc_s.so.1 (0x00001479d9dbe000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00001479cff6b000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00001479cfd67000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00001479cfb48000)
        librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00001479cf940000)
        /lib64/ld-linux-x86-64.so.2 (0x00001479d9d36000)
        libopen-pal.so.80 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./libopen-pal.so.80 (0x00001479cf87f000)
        libpmix.so.2 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./libpmix.so.2 (0x00001479cf700000)
        libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00001479cf4fd000)
        libevent_core-2.1.so.7 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./libevent_core-2.1.so.7 (0x00001479d9d82000)
        libevent_pthreads-2.1.so.7 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./libevent_pthreads-2.1.so.7 (0x00001479d9d7d000)
        libhwloc.so.15 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./libhwloc.so.15 (0x00001479cf4a3000)
        libxml2.so.2 => /home/kandpal/bin/anaconda3/envs/alamode/lib/././libxml2.so.2 (0x00001479cf33a000)
        libiconv.so.2 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./././libiconv.so.2 (0x00001479cf253000)
        libz.so.1 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./././libz.so.1 (0x00001479d9d60000)
        liblzma.so.5 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./././liblzma.so.5 (0x00001479cf223000)
        libicui18n.so.73 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./././libicui18n.so.73 (0x00001479ceee8000)
        libicuuc.so.73 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./././libicuuc.so.73 (0x00001479cecda000)
        libicudata.so.73 => /home/kandpal/bin/anaconda3/envs/alamode/lib/./././libicudata.so.73 (0x00001479cce4b000)
(alamode) kandpal@ws158:~$

ttadano Feb 14, 2024
Maintainer

The MKL library installed under /opt/intel/oneapi/mkl is linked instead of anaconda's distribution of MKL. This potentially causes the error.

If you haven't installed mkl in anaconda, please run conda install -c conda-forge mkl and rebuild anphon. When you do so, please check if the CMake can correctly detect anaconda's blas and lapack instead of those under /opt/intel/oneapi/mkl .

16-vikrant Feb 14, 2024

The error is still there. I am pasting the output cmake, make, and test here.

cmake ..

(alamode) kandpal@ws158:~/alamode/_build$ cmake ..
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


-- The C compiler identification is GNU 12.3.0
-- The CXX compiler identification is GNU 12.3.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/kandpal/bin/anaconda3/envs/alamode/bin/x86_64-conda-linux-gnu-cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/kandpal/bin/anaconda3/envs/alamode/bin/x86_64-conda-linux-gnu-c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Deprecation Warning at alm/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


Setting up for ALM code (ALAMODE version: 1.4.2)
SPGLIB_ROOT is not given by -DSPGLIB_ROOT option. Just add -lsymspg.
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found Boost: /home/kandpal/bin/anaconda3/envs/alamode/lib/cmake/Boost-1.84.0/BoostConfig.cmake (found version "1.84.0")
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /home/kandpal/bin/anaconda3/envs/alamode/lib/libmkl_intel_lp64.so;/home/kandpal/bin/anaconda3/envs/alamode/lib/libmkl_intel_thread.so;/home/kandpal/bin/anaconda3/envs/alamode/lib/libmkl_core.so;/home/kandpal/bin/anaconda3/envs/alamode/lib/libiomp5.so;-lpthread;-lm;-ldl
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /home/kandpal/bin/anaconda3/envs/alamode/lib/libmkl_intel_lp64.so;/home/kandpal/bin/anaconda3/envs/alamode/lib/libmkl_intel_thread.so;/home/kandpal/bin/anaconda3/envs/alamode/lib/libmkl_core.so;/home/kandpal/bin/anaconda3/envs/alamode/lib/libiomp5.so;-lpthread;-lm;-ldl;-lpthread;-lm;-ldl
CMake Deprecation Warning at anphon/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


Setting up for ANPHON code (ALAMODE version: 1.4.2)
-- Found MPI_C: /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- dir='/home/kandpal/bin/anaconda3/envs/alamode/include'
-- dir='/home/kandpal/bin/anaconda3/envs/alamode/include/eigen3'
-- dir='/home/kandpal/bin/anaconda3/envs/alamode/include'
MPI_C_LIBRARIES = /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so
MPI_CXX_LIBRARIES = /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so
CMake Deprecation Warning at tools/CMakeLists.txt:1 (cmake_minimum_required):
  Compatibility with CMake < 3.5 will be removed from a future version of
  CMake.

  Update the VERSION argument <min> value or use a ...<max> suffix to tell
  CMake that the project does not need compatibility with older versions.


Setting up for TOOLS (ALAMODE version: 1.4.2)
-- Configuring done (6.2s)
-- Generating done (0.0s)
-- Build files have been written to: /home/kandpal/alamode/_build

make

(alamode) kandpal@ws158:~/alamode/_build$ make -j
[  1%] Building CXX object tools/CMakeFiles/analyze_phonons.dir/analyze_phonons.cpp.o
[  3%] Building CXX object tools/CMakeFiles/fc_virtual.dir/fc_virtual.cpp.o
[  7%] Building CXX object tools/CMakeFiles/parse_fcsxml.dir/parse_fcsxml.cpp.o
[  7%] Building CXX object alm/CMakeFiles/alm.dir/main.cpp.o
[  9%] Building CXX object tools/CMakeFiles/qe2alm.dir/qe2alm.cpp.o
[ 11%] Building CXX object tools/CMakeFiles/dfc2.dir/dfc2.cpp.o
[ 13%] Building CXX object anphon/CMakeFiles/anphon.dir/conductivity.cpp.o
[ 17%] Building CXX object alm/CMakeFiles/alm.dir/constraint.cpp.o
[ 17%] Building CXX object alm/CMakeFiles/alm.dir/optimize.cpp.o
[ 19%] Building CXX object anphon/CMakeFiles/anphon.dir/ewald.cpp.o
[ 21%] Building CXX object alm/CMakeFiles/alm.dir/files.cpp.o
[ 23%] Building CXX object alm/CMakeFiles/alm.dir/input_setter.cpp.o
[ 25%] Building CXX object alm/CMakeFiles/alm.dir/input_parser.cpp.o
[ 26%] Building CXX object alm/CMakeFiles/alm.dir/alm.cpp.o
[ 30%] Building CXX object anphon/CMakeFiles/anphon.dir/kpoint.cpp.o
[ 30%] Building CXX object anphon/CMakeFiles/anphon.dir/isotope.cpp.o
[ 32%] Building CXX object anphon/CMakeFiles/anphon.dir/dynamical.cpp.o
[ 34%] Building CXX object alm/CMakeFiles/alm.dir/patterndisp.cpp.o
[ 36%] Building CXX object alm/CMakeFiles/alm.dir/symmetry.cpp.o
[ 38%] Building CXX object alm/CMakeFiles/alm.dir/timer.cpp.o
[ 40%] Building CXX object anphon/CMakeFiles/anphon.dir/phonon_velocity.cpp.o
[ 42%] Building CXX object anphon/CMakeFiles/anphon.dir/integration.cpp.o
[ 44%] Building CXX object alm/CMakeFiles/alm.dir/fcs.cpp.o
[ 46%] Building CXX object alm/CMakeFiles/alm.dir/cluster.cpp.o
[ 48%] Building CXX object anphon/CMakeFiles/anphon.dir/anharmonic_core.cpp.o
[ 50%] Building CXX object anphon/CMakeFiles/anphon.dir/dielec.cpp.o
[ 53%] Building CXX object anphon/CMakeFiles/anphon.dir/gruneisen.cpp.o
[ 53%] Building CXX object anphon/CMakeFiles/anphon.dir/selfenergy.cpp.o
[ 57%] Building CXX object anphon/CMakeFiles/anphon.dir/timer.cpp.o
[ 57%] Building CXX object alm/CMakeFiles/alm.dir/alm_cui.cpp.o
[ 59%] Building CXX object anphon/CMakeFiles/anphon.dir/phonon_dos.cpp.o
[ 61%] Building CXX object anphon/CMakeFiles/anphon.dir/scph.cpp.o
[ 63%] Building CXX object anphon/CMakeFiles/anphon.dir/symmetry_core.cpp.o
[ 67%] Building CXX object anphon/CMakeFiles/anphon.dir/main.cpp.o
[ 67%] Building CXX object alm/CMakeFiles/alm.dir/writer.cpp.o
[ 69%] Building CXX object anphon/CMakeFiles/anphon.dir/parsephon.cpp.o
[ 73%] Building CXX object anphon/CMakeFiles/anphon.dir/mode_analysis.cpp.o
[ 73%] Building CXX object anphon/CMakeFiles/anphon.dir/write_phonons.cpp.o
[ 75%] Building CXX object anphon/CMakeFiles/anphon.dir/thermodynamics.cpp.o
[ 76%] Building CXX object alm/CMakeFiles/alm.dir/rref.cpp.o
[ 78%] Building CXX object anphon/CMakeFiles/anphon.dir/mpi_common.cpp.o
[ 80%] Building CXX object anphon/CMakeFiles/anphon.dir/phonons.cpp.o
[ 82%] Building CXX object anphon/CMakeFiles/anphon.dir/fcs_phonon.cpp.o
[ 84%] Building CXX object alm/CMakeFiles/alm.dir/system.cpp.o
[ 86%] Building CXX object anphon/CMakeFiles/anphon.dir/system.cpp.o
In file included from /home/kandpal/bin/anaconda3/envs/alamode/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/kandpal/bin/anaconda3/envs/alamode/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/kandpal/bin/anaconda3/envs/alamode/include/boost/math/special_functions/erf.hpp:13,
                 from /home/kandpal/alamode/anphon/ewald.cpp:27:
/home/kandpal/bin/anaconda3/envs/alamode/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
[ 88%] Linking CXX executable analyze_phonons
[ 88%] Built target analyze_phonons
[ 90%] Linking CXX executable qe2alm
[ 90%] Built target qe2alm
[ 92%] Linking CXX executable parse_fcsxml
[ 92%] Built target parse_fcsxml
[ 94%] Linking CXX executable fc_virtual
[ 94%] Built target fc_virtual
[ 96%] Linking CXX executable dfc2
[ 96%] Built target dfc2
[ 98%] Linking CXX executable anphon
[ 98%] Built target anphon
[100%] Linking CXX executable alm
[100%] Built target alm

test run

(alamode) kandpal@ws158:~/alamode/_build$ cd ../test/
(alamode) kandpal@ws158:~/alamode/test$ l
total 20K
-rwxr-xr-x 1 kandpal kandpal 8.6K Sep 28  2022 test_si.py
-rw-rw-r-- 1 kandpal kandpal  242 Sep 28  2022 README.md
drwxrwxr-x 2 kandpal kandpal 4.0K Feb 14 11:45 si
(alamode) kandpal@ws158:~/alamode/test$ python test_si.py
Silicon ALM --> pass
[ws158:41820:0:41820] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x440000e0)
==== backtrace (tid:  41820) ====
 0  /home/kandpal/bin/anaconda3/envs/alamode/lib/openmpi/../libucs.so.0(ucs_handle_error+0x2fd) [0x1493324a006d]
 1  /home/kandpal/bin/anaconda3/envs/alamode/lib/openmpi/../libucs.so.0(+0x2a264) [0x1493324a0264]
 2  /home/kandpal/bin/anaconda3/envs/alamode/lib/openmpi/../libucs.so.0(+0x2a42a) [0x1493324a042a]
 3  /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33) [0x149335ff7453]
 4  /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x10f) [0x55b2c375783f]
 5  /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS4PHONC1EiPPci+0x7d) [0x55b2c3771c4d]
 6  /home/kandpal/alamode/_build/anphon/anphon(main+0x40) [0x55b2c36cf1c0]
 7  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x1493359cac87]
 8  /home/kandpal/alamode/_build/anphon/anphon(+0x2c4a5) [0x55b2c36cf4a5]
=================================
[ws158:41820] *** Process received signal ***
[ws158:41820] Signal: Segmentation fault (11)
[ws158:41820] Signal code:  (-6)
[ws158:41820] Failing at address: 0x3e80000a35c
[ws158:41820] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef10)[0x1493359e7f10]
[ws158:41820] [ 1] /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33)[0x149335ff7453]
[ws158:41820] [ 2] /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x10f)[0x55b2c375783f]
[ws158:41820] [ 3] /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS4PHONC1EiPPci+0x7d)[0x55b2c3771c4d]
[ws158:41820] [ 4] /home/kandpal/alamode/_build/anphon/anphon(main+0x40)[0x55b2c36cf1c0]
[ws158:41820] [ 5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x1493359cac87]
[ws158:41820] [ 6] /home/kandpal/alamode/_build/anphon/anphon(+0x2c4a5)[0x55b2c36cf4a5]
[ws158:41820] *** End of error message ***
[ws158:41823:0:41823] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x440000e0)
==== backtrace (tid:  41823) ====
 0  /home/kandpal/bin/anaconda3/envs/alamode/lib/openmpi/../libucs.so.0(ucs_handle_error+0x2fd) [0x14a84482906d]
 1  /home/kandpal/bin/anaconda3/envs/alamode/lib/openmpi/../libucs.so.0(+0x2a264) [0x14a844829264]
 2  /home/kandpal/bin/anaconda3/envs/alamode/lib/openmpi/../libucs.so.0(+0x2a42a) [0x14a84482942a]
 3  /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33) [0x14a848380453]
 4  /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x10f) [0x563ae838f83f]
 5  /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS4PHONC1EiPPci+0x7d) [0x563ae83a9c4d]
 6  /home/kandpal/alamode/_build/anphon/anphon(main+0x40) [0x563ae83071c0]
 7  /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x14a847d53c87]
 8  /home/kandpal/alamode/_build/anphon/anphon(+0x2c4a5) [0x563ae83074a5]
=================================
[ws158:41823] *** Process received signal ***
[ws158:41823] Signal: Segmentation fault (11)
[ws158:41823] Signal code:  (-6)
[ws158:41823] Failing at address: 0x3e80000a35f
[ws158:41823] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x3ef10)[0x14a847d70f10]
[ws158:41823] [ 1] /home/kandpal/bin/anaconda3/envs/alamode/lib/libmpi.so.40(MPI_Comm_rank+0x33)[0x14a848380453]
[ws158:41823] [ 2] /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x10f)[0x563ae838f83f]
[ws158:41823] [ 3] /home/kandpal/alamode/_build/anphon/anphon(_ZN7PHON_NS4PHONC1EiPPci+0x7d)[0x563ae83a9c4d]
[ws158:41823] [ 4] /home/kandpal/alamode/_build/anphon/anphon(main+0x40)[0x563ae83071c0]
[ws158:41823] [ 5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0x14a847d53c87]
[ws158:41823] [ 6] /home/kandpal/alamode/_build/anphon/anphon(+0x2c4a5)[0x563ae83074a5]
[ws158:41823] *** End of error message ***
Traceback (most recent call last):
  File "test_si.py", line 283, in <module>
    info = runtest_silicon(almbin, anphonbin, project_root)
  File "test_si.py", line 258, in runtest_silicon
    info = check_consistency_anphon(project_root, abs_tol=0.1, rel_tol=0.01)
  File "test_si.py", line 194, in check_consistency_anphon
    data_now = np.loadtxt('si222.bands')
  File "/home/kandpal/.local/lib/python3.7/site-packages/numpy/lib/npyio.py", line 1067, in loadtxt
    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
  File "/home/kandpal/.local/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 193, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)
  File "/home/kandpal/.local/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 533, in open
    raise IOError("%s not found." % path)
OSError: si222.bands not found.
(alamode) kandpal@ws158:~/alamode/test$

ttadano Feb 14, 2024
Maintainer

It seems that the error is related to the ucx https://openucx.readthedocs.io/en/master/running.html of OpenMPI.

Please consider changing the mpirun options so that the ucx pml is not used. If this fails, all I can suggest is to use intel MPI instead of OpenMPI.

16-vikrant Feb 14, 2024

Dear @ttadano

Thank you for your quick response. I removed OpenMPI, and finally, it is working. I've attached the screenshot of the test run.

Again, thank you very much for your support.

Namaste
Vikrant

QuaziBhoi · 2024-06-30T14:24:01Z

QuaziBhoi
Jun 30, 2024

Dear @ttadano

I am still facing this issue. I could not resolve it following the previous posts. Can you please help?

8 replies

QuaziBhoi Jul 2, 2024

ttadano Jul 2, 2024
Maintainer

Do you know why mkl is linked instead of openblas? Also, can you check if the linked libmpi.so is from openmpi or intel MPI?

QuaziBhoi Jul 3, 2024

Apologies for the late reply, I have been able to link openblas. The linked libmpi.so is from openmpi. I have been trying to replace it with Intel MPI but have been unsuccessful so far. Should I completely remove openmpi from my system?

ttadano Jul 4, 2024
Maintainer

Do you still see the same error when the openblas is linked instead of MKL?

Indeed, I still do not understand why the error occurs in your environment. The compilation procedure looks fine. In my environment, similar to yours (Ubuntu 22.04 LTS), I did not see the issue. Perhaps a compatibility issue specific to some conda-installed libraries causes the issue, but I am not very sure.

QuaziBhoi Jul 8, 2024

Many thanks for your support. Although I failed to integrate Intel MPI into the build, I was able to make it word by removing OpenMPI completely from my system by using:

conda remove openmpi
cd alamode
rm -rf _build
mkdir _build; cd _build
cmake -DUSE_MKL_FFT=no ..
make -j

cmake still links to an old version of OpenMPI, but anphon works now.

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compile problem #121

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when using the binaries, it may be necessary to set $LD_LIBRARY_PATH as**

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