installation on a fresh ubuntu VM results in error
agrero opened this issue · comments
I am attempting to install espresso++ onto a fresh Ubuntu virtual machine but have been running into issues. I am following the quick install (as well as the ubuntu specific install instructions) as outlined on the github. Currently I am running into an error “CMake Error at CMakeLists.txt:72 (message): HDF5 with MPI support is required! Serial version detected.” I’ve checked my hdf5 config and it shoes that the parallel version is activated, but the error still persists.
@agrero apt install libhdf5-103 or try to re-install
libhdf5-103 is the serial version, which was found already, I think libhdf5-openmpi-dev is missing here.
will that not also install libhdf5-openmpi-xxx meanwhile and by default? I can't remember. Anyhow, libhdf5-openmpi-xxx is the one @agrero you should have
$dpkg -l | grep hdf5
ii hdf5-helpers 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - Helper tools
ii libhdf5-103:amd64 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-cpp-103:amd64 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - C++ libraries
ii libhdf5-dev 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - development files - serial version
ii libhdf5-openmpi-103:amd64 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii libhdf5-openmpi-dev 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - development files - OpenMPI version
And it does not necessarily need to be version 103 any recent hdf5 version will do.
I do have libhdf5-openmpi-103:amd64 installed as well as the serialized version. I'm guessing the program is just still pointing to the serialized version, should I uninstall the serialized version?
I do have libhdf5-openmpi-103:amd64 installed as well as the serialized version. I'm guessing the program is just still pointing to the serialized version, should I uninstall the serialized version?
I guess so. For the safest, try
sudo apt remove libhdf5*
sudo apt autoremove
sudo apt libhdf5-openmpi-dev
Assuming you meant to have install before the libhdf5 call in that last line there, it now sends a different error message making me think it can't find the package at all. I will post this below.
CMake Error at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS
HDF5_HL_LIBRARIES C HL) (found version "")
Call Stack (most recent call first):
/usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
cmake/FindHDF5.cmake:1001 (find_package_handle_standard_args)
CMakeLists.txt:70 (find_package)
hmmm, the following Dockerfile builds successfully
FROM ubuntu:22.04
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get update \
&& apt-get install -y\
build-essential \
clang-format \
cmake \
curl \
doxygen \
ghostscript \
git \
graphviz \
ipython3 \
libboost-all-dev \
libfftw3-dev \
libgromacs-dev \
libhdf5-dev \
libhdf5-openmpi-dev \
openmpi-bin \
python3-dev \
python3-h5py \
python3-matplotlib \
python3-mpi4py \
python3-numpy \
python3-pip \
sphinx-common \
sudo \
wget \
&& rm -rf /var/lib/apt/lists/*
RUN git clone https://github.com/espressopp/espressopp.git \
&& cmake -S espressopp -B espressopp-build -DCMAKE_BUILD_TYPE=Release \
&& cmake --build espressopp-build --parallel 4