Issue when installing band_cal_parallel

[HongzhenZhong]

Dear HamGNN Team,

I hope this message finds you well. I am currently facing an issue when trying to install the band_cal_parallel module. During installation, I encountered multiple compilation errors related to missing files and dependencies.

Below is the full error message I received:

(band_cal_parallel) sch9368@ln2:~/soft/HamGNN-main/band_cal_parallel$ pip install --force-reinstall band_cal_parallel-0.1.15-py3-none-any.whl
Processing ./band_cal_parallel-0.1.15-py3-none-any.whl
Collecting numpy (from band-cal-parallel==0.1.15)
Using cached numpy-2.0.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (60 kB)
Collecting torch (from band-cal-parallel==0.1.15)
Downloading torch-2.6.0-cp39-cp39-manylinux1_x86_64.whl.metadata (28 kB)
Collecting torch-geometric (from band-cal-parallel==0.1.15)
Downloading torch_geometric-2.6.1-py3-none-any.whl.metadata (63 kB)
Collecting pymatgen (from band-cal-parallel==0.1.15)
Using cached pymatgen-2024.8.9-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting mpitool (from band-cal-parallel==0.1.15)
Using cached mpitool-0.0.1-cp39-cp39-manylinux1_x86_64.whl.metadata (113 bytes)
Collecting joblib>=1 (from pymatgen->band-cal-parallel==0.1.15)
Downloading joblib-1.5.2-py3-none-any.whl.metadata (5.6 kB)
Collecting matplotlib>=3.8 (from pymatgen->band-cal-parallel==0.1.15)
Using cached matplotlib-3.9.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
Collecting monty>=2024.7.29 (from pymatgen->band-cal-parallel==0.1.15)
Using cached monty-2025.3.3-py3-none-any.whl.metadata (3.6 kB)
Collecting networkx>=2.2 (from pymatgen->band-cal-parallel==0.1.15)
Using cached networkx-3.2.1-py3-none-any.whl.metadata (5.2 kB)
Collecting palettable>=3.3.3 (from pymatgen->band-cal-parallel==0.1.15)
Using cached palettable-3.3.3-py2.py3-none-any.whl.metadata (3.3 kB)
Collecting pandas>=2 (from pymatgen->band-cal-parallel==0.1.15)
Downloading pandas-2.3.3.tar.gz (4.5 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.5/4.5 MB 33.4 kB/s 0:02:05
Installing build dependencies ... done
Getting requirements to build wheel ... done
Installing backend dependencies ... done
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [215 lines of output]
+ meson setup /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8 /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/.mesonpy-c9mstqyl -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --vsenv --native-file=/tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/.mesonpy-c9mstqyl/meson-python-native-file.ini
The Meson build system
Version: 1.9.1
Source dir: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8
Build dir: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/.mesonpy-c9mstqyl
Build type: native build
Project name: pandas
Project version: 2.3.3
C compiler for the host machine: cc (gcc 4.8.5 "cc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)")
C linker for the host machine: cc ld.bfd 2.27-44
C++ compiler for the host machine: c++ (gcc 4.8.5 "c++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)")
C++ linker for the host machine: c++ ld.bfd 2.27-44
Cython compiler for the host machine: cython (cython 3.1.4)
Host machine cpu family: x86_64
Host machine cpu: x86_64
Program python found: YES (/public1/home/sch9368/anaconda3/envs/DeepH-pack/bin/python3.9)
Found pkg-config: YES (/usr/bin/pkg-config) 0.27.1
Run-time dependency python found: YES 3.9
Build targets in project: 53

  pandas 2.3.3
  
    User defined options
      Native files: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/.mesonpy-c9mstqyl/meson-python-native-file.ini
      b_ndebug    : if-release
      b_vscrt     : md
      buildtype   : release
      vsenv       : true
  
  Found ninja-1.13.1 at /public1/home/sch9368/anaconda3/envs/DeepH-pack/bin/ninja
  
  Visual Studio environment is needed to run Ninja. It is recommended to use Meson wrapper:
  /tmp/pip-build-env-dtxnbyr5/overlay/bin/meson compile -C .
  + /public1/home/sch9368/anaconda3/envs/DeepH-pack/bin/ninja
  [1/151] Generating pandas/_libs/index_class_helper_pxi with a custom command
  [2/151] Generating pandas/_libs/intervaltree_helper_pxi with a custom command
  [3/151] Generating pandas/_libs/khash_primitive_helper_pxi with a custom command
  [4/151] Generating pandas/_libs/sparse_op_helper_pxi with a custom command
  [5/151] Generating pandas/_libs/algos_take_helper_pxi with a custom command
  [6/151] Generating pandas/_libs/algos_common_helper_pxi with a custom command
  [7/151] Generating pandas/_libs/hashtable_class_helper_pxi with a custom command
  [8/151] Generating pandas/_libs/hashtable_func_helper_pxi with a custom command
  [9/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/byteswap.pyx
  [10/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/ops_dispatch.pyx
  [11/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/properties.pyx
  [12/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/base.pyx
  [13/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/indexing.pyx
  [14/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/ccalendar.pyx
  [15/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/dtypes.pyx
  [16/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/testing.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [17/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/missing.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [18/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/np_datetime.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [19/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/nattype.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/nattype.pyx:79:0: Global name __nat_unpickle matched from within class scope in contradiction to Python 'class private name' rules. This may change in a future release.
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/nattype.pyx:79:0: Global name __nat_unpickle matched from within class scope in contradiction to Python 'class private name' rules. This may change in a future release.
  [20/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/arrays.pyx
  [21/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/sas.pyx
  [22/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/window/indexers.pyx
  [23/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/ops.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [24/151] Compiling C object pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_datetime_date_conversions.c.o
  [25/151] Compiling C object pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime.c.o
  FAILED: [code=1] pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime.c.o
  cc -Ipandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs -I../pandas/_libs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime.c.o -MF pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime.c.o.d -o pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime.c.o -c ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c:57:1: error: static assertion failed: "__has_builtin not detected; please try a newer compiler"
   _Static_assert(0, "__has_builtin not detected; please try a newer compiler");
   ^
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c: In function ‘scaleYearToEpoch’:
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c:343:3: warning: implicit declaration of function ‘checked_int64_sub’ [-Wimplicit-function-declaration]
     return checked_int64_sub(year, 1970, result);
     ^
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c: In function ‘scaleYearsToMonths’:
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c:347:3: warning: implicit declaration of function ‘checked_int64_mul’ [-Wimplicit-function-declaration]
     return checked_int64_mul(years, 12, result);
     ^
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c: In function ‘npy_datetimestruct_to_datetime’:
  ../pandas/_libs/src/vendored/numpy/datetime/np_datetime.c:425:5: warning: implicit declaration of function ‘checked_int64_add’ [-Wimplicit-function-declaration]
       PD_CHECK_OVERFLOW(checked_int64_add(months, months_adder, &months));
       ^
  [26/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/hashing.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [27/151] Compiling C object pandas/_libs/pandas_parser.cpython-39-x86_64-linux-gnu.so.p/src_parser_io.c.o
  [28/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/tzconversion.pyx
  [29/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/reshape.pyx
  [30/151] Compiling C object pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_datetime_pd_datetime.c.o
  [31/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/vectorized.pyx
  [32/151] Compiling C object pandas/_libs/pandas_datetime.cpython-39-x86_64-linux-gnu.so.p/src_vendored_numpy_datetime_np_datetime_strings.c.o
  [33/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/timezones.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [34/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/fields.pyx
  [35/151] Compiling C object pandas/_libs/pandas_parser.cpython-39-x86_64-linux-gnu.so.p/src_parser_pd_parser.c.o
  [36/151] Compiling C object pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_indexing.pyx.c.o
  FAILED: [code=1] pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_indexing.pyx.c.o
  cc -Ipandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs -I../pandas/_libs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_indexing.pyx.c.o -MF pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_indexing.pyx.c.o.d -o pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_indexing.pyx.c.o -c pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/indexing.pyx.c
  pandas/_libs/indexing.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/indexing.pyx.c:1344:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [37/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslib.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [38/151] Compiling C object pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_arrays.pyx.c.o
  FAILED: [code=1] pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_arrays.pyx.c.o
  cc -Ipandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs -I../pandas/_libs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_arrays.pyx.c.o -MF pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_arrays.pyx.c.o.d -o pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_arrays.pyx.c.o -c pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/arrays.pyx.c
  pandas/_libs/arrays.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/arrays.pyx.c:1422:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [39/151] Compiling C object pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_base.pyx.c.o
  FAILED: [code=1] pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_base.pyx.c.o
  cc -Ipandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs/tslibs -I../pandas/_libs/tslibs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_base.pyx.c.o -MF pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_base.pyx.c.o.d -o pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_base.pyx.c.o -c pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/base.pyx.c
  pandas/_libs/tslibs/base.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/base.pyx.c:1375:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [40/151] Compiling C object pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_np_datetime.pyx.c.o
  FAILED: [code=1] pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_np_datetime.pyx.c.o
  cc -Ipandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs/tslibs -I../pandas/_libs/tslibs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_np_datetime.pyx.c.o -MF pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_np_datetime.pyx.c.o.d -o pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_np_datetime.pyx.c.o -c pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/np_datetime.pyx.c
  pandas/_libs/tslibs/np_datetime.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/np_datetime.pyx.c:1411:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [41/151] Compiling C object pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_ccalendar.pyx.c.o
  FAILED: [code=1] pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_ccalendar.pyx.c.o
  cc -Ipandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs/tslibs -I../pandas/_libs/tslibs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_ccalendar.pyx.c.o -MF pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_ccalendar.pyx.c.o.d -o pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_ccalendar.pyx.c.o -c pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/ccalendar.pyx.c
  pandas/_libs/tslibs/ccalendar.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/ccalendar.pyx.c:1377:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [42/151] Compiling C object pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_dtypes.pyx.c.o
  FAILED: [code=1] pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_dtypes.pyx.c.o
  cc -Ipandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs/tslibs -I../pandas/_libs/tslibs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_dtypes.pyx.c.o -MF pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_dtypes.pyx.c.o.d -o pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_dtypes.pyx.c.o -c pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/dtypes.pyx.c
  pandas/_libs/tslibs/dtypes.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/dtypes.pyx.c:1408:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [43/151] Compiling C object pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_missing.pyx.c.o
  FAILED: [code=1] pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_missing.pyx.c.o
  cc -Ipandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs -I../pandas/_libs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_missing.pyx.c.o -MF pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_missing.pyx.c.o.d -o pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_missing.pyx.c.o -c pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/missing.pyx.c
  pandas/_libs/missing.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/missing.pyx.c:1412:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [44/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/conversion.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [45/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/strptime.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [46/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/internals.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [47/151] Compiling C object pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_nattype.pyx.c.o
  FAILED: [code=1] pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_nattype.pyx.c.o
  cc -Ipandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p -Ipandas/_libs/tslibs -I../pandas/_libs/tslibs -I../../../pip-build-env-dtxnbyr5/overlay/lib/python3.9/site-packages/numpy/_core/include -I../pandas/_libs/include -I/public1/home/sch9368/anaconda3/envs/DeepH-pack/include/python3.9 -fvisibility=hidden -DNDEBUG -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -std=c11 -O3 -DNPY_NO_DEPRECATED_API=0 -DNPY_TARGET_VERSION=NPY_1_21_API_VERSION -fPIC -MD -MQ pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_nattype.pyx.c.o -MF pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_nattype.pyx.c.o.d -o pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/meson-generated_pandas__libs_tslibs_nattype.pyx.c.o -c pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/nattype.pyx.c
  pandas/_libs/tslibs/nattype.cpython-39-x86_64-linux-gnu.so.p/pandas/_libs/tslibs/nattype.pyx.c:1410:27: fatal error: stdatomic.h: No such file or directory
       #include <stdatomic.h>
                             ^
  compilation terminated.
  [48/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/window/aggregations.pyx
  [49/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/writers.pyx
  [50/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/parsing.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [51/151] Compiling C object pandas/_libs/tslibs/parsing.cpython-39-x86_64-linux-gnu.so.p/.._src_parser_tokenizer.c.o
  [52/151] Compiling C object pandas/_libs/lib.cpython-39-x86_64-linux-gnu.so.p/src_parser_tokenizer.c.o
  [53/151] Compiling C object pandas/_libs/pandas_parser.cpython-39-x86_64-linux-gnu.so.p/src_parser_tokenizer.c.o
  [54/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/parsers.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/parsers.pyx:1605:18: noexcept clause is ignored for function returning Python object
  [55/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/timestamps.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [56/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/timedeltas.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [57/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/period.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [58/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/offsets.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [59/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/lib.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [60/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/index.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [61/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/sparse.pyx
  [62/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/interval.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [63/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/join.pyx
  [64/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/hashtable.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [65/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/groupby.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  [66/151] Compiling Cython source /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/algos.pyx
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:188:38: noexcept clause is ignored for function returning Python object
  warning: /tmp/pip-install-bkam5ugs/pandas_6f6310450c734bfc8c486c2f245424e8/pandas/_libs/tslibs/util.pxd:193:40: noexcept clause is ignored for function returning Python object
  ninja: build stopped: subcommand failed.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

[QuantumLab-ZY]

Hi @HongzhenZhong,

Could you please confirm that your Python environment was set up according to the instructions in our README? In our provided environment, the installation of band_cal_parallel completes successfully without any errors. Typically, no additional dependencies are required, as all necessary packages are already included in the provided environment.

Best,
Yang Zhong

[HongzhenZhong]

Thank you for your reply. I appreciate your help.

Just to clarify, when you mention the "provided environment" in the README, is this referring to the HamGNN environment specifically? I want to ensure that my setup aligns with the environment where band_cal_parallel is known to install without issues.

[QuantumLab-ZY]

We recommend using Method 1, as this pre-built environment is the one we use most frequently and has been thoroughly tested.

Method 1: Use Pre-built Environment (Recommended)

1. Download the pre-built HamGNN Conda environment (ML.tar.gz) from [Zenodo](https://zenodo.org/records/11064223).

2. Extract it to the envs directory in your Conda installation path:

   tar -xzvf ML.tar.gz -C $HOME/miniconda3/envs/

3. Activate the environment:

   conda activate ML

This environment contains all the required dependencies and configurations, ensuring compatibility and smooth execution of HamGNN.

[HongzhenZhong]

Dear Yang Zhong,

Thank you for your continued support. I was able to set up the ML environment as per your instructions and successfully install band_cal_parallel. However, I am encountering an ImportError when trying to execute the program. Below is the error message:

mpirun -np 1 band_cal_parallel --config band_cal_parallel.yaml
Traceback (most recent call last):
File "/public1/home/sch9368/anaconda3/envs/ML/bin/band_cal_parallel", line 3, in
from HamTool.band_cal_parallel import main
File "/public1/home/sch9368/anaconda3/envs/ML/lib/python3.9/site-packages/HamTool/band_cal_parallel.py", line 8, in
from scipy.linalg import eigvalsh, eig, eigh
File "/public1/home/sch9368/anaconda3/envs/ML/lib/python3.9/site-packages/scipy/linalg/init.py", line 213, in
from ._sketches import *
File "/public1/home/sch9368/anaconda3/envs/ML/lib/python3.9/site-packages/scipy/linalg/_sketches.py", line 9, in
from scipy.sparse import csc_matrix
File "/public1/home/sch9368/anaconda3/envs/ML/lib/python3.9/site-packages/scipy/sparse/init.py", line 228, in
from .csr import *
File "/public1/home/sch9368/anaconda3/envs/ML/lib/python3.9/site-packages/scipy/sparse/csr.py", line 10, in
from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks,
ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /public1/home/sch9368/anaconda3/envs/ML/lib/python3.9/site-packages/scipy/sparse/_sparsetools.cpython-39-x86_64-linux-gnu.so)

Could you please advise on how to resolve this issue? Thank you for your time and assistance!

[QuantumLab-ZY]

This issue is caused by an outdated libstdc++.so.6 library in your Linux system environment, which lacks the CXXABI_1.3.9 symbol version required by the application.

[HongzhenZhong]

Thank you for your supporting. After resolving the previous issue, I am now encountering a new error when running band_cal_parallel. Below is the error message:

mpirun -np 1 band_cal_parallel --config band_cal_parallel.yaml
Traceback (most recent call last):
File "/HOME/scw6345/.conda/envs/ML/bin/band_cal_parallel", line 5, in
from HamTool.band_cal_parallel import main
File "/HOME/scw6345/.conda/envs/ML/lib/python3.9/site-packages/HamTool/band_cal_parallel.py", line 19, in
from mpi4py import MPI
ImportError: libmpifort.so.12: cannot open shared object file: No such file or directory

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.

---

mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

Process name: [[33212,1],0]
Exit code: 1

It seems that the program cannot locate the libmpifort.so.12 file, which is causing the error.

To help diagnose the issue, here are the details of my MPI setup:

MPI library: OpenMPI/4.1.1_gcc9.3_ucx1.14.1_cuda11.8

MPI version: 4.1.1

Could you kindly provide guidance on how to resolve this? Is there a specific MPI library or version I need to install or configure to fix this issue?

Thank you again for your assistance.

[QuantumLab-ZY]

Please make sure that all MPI-related environment variables are correctly loaded before running your program. If the issue persists even after confirming the environment setup, you can try the solution described in this blog post: https://blog.csdn.net/strawberry47/article/details/126251090 and see if it helps resolve the issue.

[HongzhenZhong]

Thank you for your previous guidance. I have now successfully reinstalled the environment and resolved the earlier MPI-related issue. The installation and execution of band_cal_parallel now proceed without MPI errors.

However, when I run the program, I encounter the following MKL-related error:

mpirun -np 1 band_cal_parallel --config band_cal_parallel.yaml
Traceback (most recent call last):
File "/HOME/scw6345/.conda/envs/HamGNN_2.1/bin/band_cal_parallel", line 3, in
from HamTool.band_cal_parallel import main
File "/HOME/scw6345/.conda/envs/HamGNN_2.1/lib/python3.9/site-packages/HamTool/band_cal_parallel.py", line 21, in
import mpitool
ImportError: /data/apps/intel/2021/mkl/latest/lib/intel64/libmkl_sequential.so.1: undefined symbol: mkl_sparse_z_bsr_ng_avx521_sp_mv_i4

It seems that there is an issue related to the MKL library. Following is the MKL version I used:

mkl 2021.4.0 h8d4b97c_729 conda-forge
mkl-devel 2021.4.0 ha770c72_730 conda-forge
mkl-include 2021.4.0 h8d4b97c_729 conda-forge
mkl-service 2.4.0 py39h7e14d7c_0 conda-forge
mkl_fft 1.3.1 py39h0c7bc48_1 conda-forge
mkl_random 1.2.2 py39hde0f152_0 conda-forge

Could you please advise on whether band_cal_parallel is compatible with this MKL version, or if it should instead use the MKL version bundled within the provided environment?

Thank you very much for your time and assistance.

[QuantumLab-ZY]

Maybe you can refer to GitHub Issues #18 and #12 for solutions.