Frequently Asked Questions

Installation

What is the tddft=yes?

Support real-time TDDFT by using ce-tddft. And the real-time TDDFT also support adding/replacing external potential.

Running

Some Intel MKL errors occur. What do I do?

Try:

export LD_PRELOAD=/opt/intel/oneapi/mkl/latest/lib/libmkl_rt.so

Some Intel MPI errors occur.

Try:

export LD_PRELOAD=/opt/intel/oneapi/mpi/latest/lib/libmpifort.so

Why can’t I read the wavefunctions? Why does it hang?

There are two different ways to store wavefunctions in QE, which is controls by PW parameter wf_collect. In doubt, simply use one processor to read.
If the wavefunctions were stored by old version QE (<6.4) or eQE, please use the old version of QEpy by:
```
python -m pip install qepy==6.5.0
```

Some f90wrap errors occur. What do I do?

Please try install the latest f90wrap . e.g.
python -m pip install --upgrade f90wrap

Signal: Segmentation fault...

QEpy and mpi4py should installed with same compiler. If not, try reinstall the mpi4py by:
```
python -m pip install mpi4py --no-cache-dir
```

BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES

Without mpi4py, the QEpy still can parallel running, but you cannot control the parallel. If you want to run a different job, you have to restart the script or the jupyter kernel. With mpi4py to run the parallel QEpy, you can add comm to Driver, or directly use comm.py2f() in the function.

Bugs

GCC

For new version of gcc (eg. gcc=11.2) with LTO supported or under conda environment, if you met the problem when you install the QEpy:

lto1: fatal error:...

Try disable link-time-optimization by add -fno-lto to the variable FFLAGS and CFLAGS.

Gfortran

For gfortran>=10.0 sometimes still works, but will has error:

Type mismatch between actual argument...

Try to add -fallow-argument-mismatch to the variable FFLAGS (e.g. FFLAGS='-fPIC -fallow-argument-mismatch').

For a few versions of BLAS library, will raise error:

Segmentation fault - invalid memory reference...

This is due to the zdotc function of external libraries. More details to here. One solution is append the -ff2c to CFLAGS of QE. For example, the following can be used for MacOS with Apple silicon:
./configure FFLAGS='-fPIC -fallow-argument-mismatch -ff2c -fno-second-underscore' CFLAGS='-fPIC -arch arm64' CPP='gcc -E' LDFLAGS=-headerpad_max_install_names

Intel Compiler

If you met any problems like the following, please try a newer Intel compiler or GNU compiler.

[MPID_nem_tmi_pending_ssend_dequeue]: ERROR: can not find matching ssend...

The initial density totally wrong with more than one nodes.

The gcc version between 4.8-9.2 are supported by intel compiler, which upgraded until 2022.1 version. More details to here.

...error: attribute "__malloc__" does not take arguments...

OpenMPI

If you met some problems like the following:

mca_base_component_repository_open: unable to open mca_patcher_overwrite...

Please update to latest version of OpenMPI, or fix with patchelf (openmpi=2.1.1):
#!/bin/sh
prefix="/usr/lib/x86_64-linux-gnu/openmpi"
for filename in $(ls $prefix/lib/openmpi/*.so); do
    patchelf --add-needed libmpi.so.20 $filename
    patchelf --set-rpath "\$ORIGIN/.." $filename
done

MacOS

For some versions of the MacOS, maybe you will has error:

Illegal Instruction: 4...

Try to add -mmacosx-version-min=10.14 to the FFLAGS.

clang: error: no input files...

Redefine CPP as CPP=gcc -E in make.inc.

changing install names or rpaths can't be redone for...

Add -headerpad_max_install_names to the LDFLAGS.

QE

compilation aborted for mbd_c_api.F90

ifx not works for mbd until #60. The easiest way to fix is running the following before make
export LIBMBD_C_API=0

Abandon

Read old format XML file

The old format (-D__OLDXML) has been deprecated since version 6.4. oldxml allows you to read the output (wavefunctions, etc) from an old XML file. Last version to support it is qepy==6.5.0.