Installation requirements question

[EricAComstock]

Hello All,

I am reaching out because I have had trouble installing Vlasiator, and had a few questions.
a) What are the main system requirements for Vlasiator to be installed and run successfully?
b) Can Vlasiator be installed on any folder, or are there specific location requirements?
c) How do I link the builds of the Vlasiator dependencies to Vlasiator?
d) Are the dependency repositories on the wiki still up to date? I was unable to install phiprof from the url given.

Sincerely,
Eric A. Comstock

[veetihaaja]

Hello Eric,

There's no standard minimum system requirements for Vlasiator, as that would really depend on what you want to simulate. The simplest 1D (in space) simulations can be run with a regular laptop, but more complicated 3D simulations are only feasible on compute clusters with hundreds of gigs of RAM. Memory is the biggest limiter here, and how much you need for your desired testcase is most easily found by trial and error.

There is no specific install locations necessary.

Linking to dependency libraries is done by specifying the library path in the chosen makefile. For a generic linux machine, Makefile.cubbli20 should work, where LIBRARY_PREFIX is variable pointing to library installation location. To compile Vlasiator with this specific makefile, the environment variable VLASIATOR_ARCH should be set to "cubbli20". To run on a specific compute cluster might need more work, although we do also have makefiles for some specific machines we have used, which might work with some tweaking.

Downloading libraries is easiest with the fetch_and_build_libraries.sh script provided, as the wiki might not be up to date.

Please let us know if you have any additional problems with getting Vlasiator running. If you have a specific simulation configuration you would like to run, our pre-specified projects might be of help.

-Veeti Haaja

[EricAComstock]

Hello Veeti Haaja,

Thank you! I will try that, and let you know if I run into any issues.

Sincerely
Eric A. Comstock

[EricAComstock]

Hello,

Might I ask which makefile I should use? Is there a guide somewhere do what changes to the makefile need to be made? I am using Ubuntu 24.04.4 LTS.

I have access to a computer with 1 TB of RAM, so hopefully I will have enough for 3D simulations.

Sincerely
Eric A. Comstock

[veetihaaja]

Hey,

Like I mentioned, https://github.com/fmihpc/vlasiator/blob/master/MAKE/Makefile.cubbli20 should be the easiest to get working. There doesnt exist a guide to modifying a makefile to be suitable, but with some trial and error and reading compiler (we use gcc) errors, you should be able to get Vlasiator to compile. The main part is getting the appropriate libraries and submodules found and linked during compile time.

-Veeti

[EricAComstock]

Hello Veeti,

Thank you for your help!

When I try to use make, I get the result\

=[Thank you for]=================================
┏┓ ╻ ╻╻╻  ╺┳┓╻┏┓╻┏━╸   ╻ ╻╻  ┏━┓┏━┓╻┏━┓╺┳╸┏━┓┏━┓╻
┣┻┓┃ ┃┃┃   ┃┃┃┃┗┫┃╺┓   ┃┏┛┃  ┣━┫┗━┓┃┣━┫ ┃ ┃ ┃┣┳┛╹
┗━┛┗━┛╹┗━╸╺┻┛╹╹ ╹┗━┛   ┗┛ ┗━╸╹ ╹┗━┛╹╹ ╹ ╹ ┗━┛╹┗╸╹
============[recommended by 9 out of 10 doctors]=

[GENERATE] version.cpp
[CC] version.cpp
[CC] memoryallocation.cpp
[CC] memory_report.cpp
In file included from spatial_cells/block_adjust_cpu.hpp:33,
                 from spatial_cells/block_adjust_wrapper.hpp:31,
                 from grid.h:27,
                 from memory_report.cpp:32:
./submodules/dccrg/dccrg.hpp: In member function ‘void dccrg::Dccrg<Cell_Data, Geometry, std::tuple<_Tp ...>, std::tuple<Additional_Neighbor_Items ...> >::induce_refines()’:
./submodules/dccrg/dccrg.hpp:9025:22: error: ‘erase_if’ is not a member of ‘std’; did you mean ‘enable_if’?
 9025 |                 std::erase_if(cells_to_refine, [this](uint64_t cell){return !this->is_local(cell);});
      |                      ^~~~~~~~
      |                      enable_if
./submodules/dccrg/dccrg.hpp: In member function ‘void dccrg::Dccrg<Cell_Data, Geometry, std::tuple<_Tp ...>, std::tuple<Additional_Neighbor_Items ...> >::override_refines()’:
./submodules/dccrg/dccrg.hpp:9357:22: error: ‘erase_if’ is not a member of ‘std’; did you mean ‘enable_if’?
 9357 |                 std::erase_if(old_donts, [this](uint64_t cell){return !this->is_local(cell);});;
      |                      ^~~~~~~~
      |                      enable_if
make: *** [Makefile:309: memory_report.o] Error 1

which I have not been able to fix.

Please advise.

Sincerely,
Eric Comstock

[JonasSuni]

Hi Eric,

Veeti is currently on holiday, so for now I'll try to help you in his stead.

Which compiler and which version of it are you using?

And do the CXXFLAGS in your makefile specify -std=c++20 or a different C++ standard?

Best regards,
Jonas Suni

[EricAComstock]

Hello Jonas,

Thank you!

I am using the default compiler, which is gcc for my system.

My make command is

make clean
make CXXFLAGS="\
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/BUILD_DIR/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/phiprof/include"

Sincerely,
Eric Comstock

[EricAComstock]

Hello Jonas,

When I instead use

make clean
make CXXFLAGS="\
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/BUILD_DIR/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/phiprof/include \
-std=c++20"

I get the error

=[Thank you for]=================================
┏┓ ╻ ╻╻╻  ╺┳┓╻┏┓╻┏━╸   ╻ ╻╻  ┏━┓┏━┓╻┏━┓╺┳╸┏━┓┏━┓╻
┣┻┓┃ ┃┃┃   ┃┃┃┃┗┫┃╺┓   ┃┏┛┃  ┣━┫┗━┓┃┣━┫ ┃ ┃ ┃┣┳┛╹
┗━┛┗━┛╹┗━╸╺┻┛╹╹ ╹┗━┛   ┗┛ ┗━╸╹ ╹┗━┛╹╹ ╹ ╹ ┗━┛╹┗╸╹
============[recommended by 9 out of 10 doctors]=

[GENERATE] version.cpp
[CC] version.cpp
[CC] memoryallocation.cpp
[CC] memory_report.cpp
[CC] backgroundfield/backgroundfield.cpp
[CC] backgroundfield/quadr.cpp
[CC] backgroundfield/dipole.cpp
[CC] backgroundfield/linedipole.cpp
[CC] backgroundfield/vectordipole.cpp
[CC] backgroundfield/constantfield.cpp
backgroundfield/constantfield.cpp:41:8: error: no declaration matches ‘double ConstantField::operator()(double, double, double, coordinate, unsigned int, coordinate) const’
   41 | double ConstantField::operator()( double x, double y, double z, coordinate component, unsigned int derivative, coordinate dcomponent) const {
      |        ^~~~~~~~~~~~~
In file included from backgroundfield/constantfield.cpp:28:
backgroundfield/constantfield.hpp:43:9: note: candidate is: ‘Real ConstantField::operator()(Real, Real, Real, coordinate, unsigned int, coordinate) const’
   43 |    Real operator()( Real x, Real y, Real z, coordinate component, unsigned int derivative, coordinate dcomponent) const;
      |         ^~~~~~~~
backgroundfield/constantfield.hpp:32:7: note: ‘class ConstantField’ defined here
   32 | class ConstantField {
      |       ^~~~~~~~~~~~~
make: *** [Makefile:319: constantfield.o] Error 1

Sincerely,
Eric Comstock

[JonasSuni]

Hi Eric,

Please try adding your CXXFLAGS to the Makefile that you copied and edited or created instead of specifying them like this at compile time. What is currently happening is that the necessary flags specified in the main makefile are being overwritten. You should only need to make changes to the MAKE/Makefile.<your machine name here> file, and then compile with a simple make.

Cheers,
Jonas

[kstppd]

Hi Eric,

Please try adding your CXXFLAGS to the Makefile that you copied and edited or created instead of specifying them like this at compile time. What is currently happening is that the necessary flags specified in the main makefile are being overwritten. You should only need to make changes to the MAKE/Makefile.<your machine name here> file, and then compile with a simple make.

Cheers, Jonas

And then remember to export VLASIATOR_ARCH=<your machine name here> .

[EricAComstock]

Hello All,

Thank you! I added the CXXFLAGS to the bottom of the Makefile, and got much further in the make command, but it still threw an error.

This time, the error was

[LINK] vlasiator
/usr/bin/ld: cannot find -lzoltan: No such file or directory
collect2: error: ld returned 1 exit status
make: *** [Makefile:360: vlasiator] Error 1

Sincerely,
Eric Comstock

[JonasSuni]

Hi Eric,

Great! Now you just need to make sure that the INC_ and LIB_ variables in the Libraries section of the makefile point to the correct paths for the libraries. So take the -I commands out of the CXXFLAGS and put them in the Libraries section under the corresponding variable names so that the main makefile can find them.

Cheers,
Jonas

[EricAComstock]

Hello All,

What do I need to put in the Makefile?

I originally had

CXXFLAGS += \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/BUILD_DIR/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/phiprof/include \
-std=c++20

, which gave me the error I showed you before. I tried

INC_ZOlTAN += /home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/src/include
LIB_ZOlTAN += /home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/src/include
INC_ZOLTAN += home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/BUILD_DIR/src/include
LIB_ZOLTAN += home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/BUILD_DIR/src/include
LIB_PROFILE += home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/phiprof/include
INC_PROFILE += home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/phiprof/include
CXXFLAGS += -std=c++20
LIBS += -lzoltan

but that immediately threw an error.

Thank you again for your help!

Sincerely,
Eric Comstock

[JonasSuni]

Hi Eric,

Could you paste the makefile that you copied and edited or created here so we can take a closer look at the issue?

Cheers,
Jonas

[EricAComstock]

Hello All,

I mainly modified the cubbli20 makefile:

# This is meant for building local copy of Vlasiator.
# It is tested with cubbli 20 but it should work on other systems as well

# This is a modified version of Makefile.yann

# There is script called configure_cubbli20.sh that will install the dependencies automatically.
# Script will create a folder called external_libs to root folder.
# The dependencies will be installed to this folder

# configure_cubbli20.sh will install follwing libs:
# 	Zoltan
# 	VLSV 
# 	DCCRG
# 	FSGRID
# 	PHIPROF
# 	Eigen
#   Vectorclass/version1

# configure_cubbli20.sh is assumed to be located at MAKE/configure_cubbli20.sh
# and you probably need to give execution permissions to it:

# sudo chmod u+x configure_cubbli20.sh

# There might be some libefa errors but they are benign.
# (Benign = pleasant and kind; not harmful or severe. dictionary.cambridge.org)

# Boost is assumend to be installed by the system package manager (e.g. apt)
# Usually following is correct but this can be modified:

INC_BOOST = -I/usr/include/boost/
LIB_BOOST = -L/usr/lib/x86_64-linux-gnu/ -lboost_program_options


# In case of there is need for optional Jmalloc
# you can install it manually and add paths here 

# Optional
INC_JEMALLOC = #-I$(LIBRARY_PREFIX)/include/jemalloc
LIB_JEMALLOC = #-L$(LIBRARY_PREFIX)/lib -ljemalloc





#======== Vectorization ==========
#Set vector backend type for vlasov solvers, sets precision and length. 
#NOTE this has to have the same precision as the distribution function define (DISTRIBUTION_FP_PRECISION)
#Options: 
# AVX:	    VEC4D_AGNER, VEC4F_AGNER, VEC8F_AGNER
# AVX512:   VEC8D_AGNER, VEC16F_AGNER
# Fallback: VEC_FALLBACK_GENERIC

ifeq ($(DISTRIBUTION_FP_PRECISION),SPF)
#Single-precision        
	VECTORCLASS = VEC8F_AGNER
else
#Double-precision
	VECTORCLASS = VEC4D_AGNER
endif


#======== Allocator =========
#Use TBB malloc

CMP = mpic++
LNK = mpic++

PAPI_FLAG =

FLAGS =
# Debug flags:
#CXXFLAGS = -g  -funroll-loops -std=c++20 -fopenmp -W -Wall -pedantic -Wno-unused -fabi-version=0 -mavx
CXXFLAGS = -O3  -funroll-loops -std=c++20 -fopenmp -W -Wall -Wno-unused -fabi-version=0 -mavx

MATHFLAGS = -ffast-math -fno-finite-math-only
testpackage: MATHFLAGS = -fno-unsafe-math-optimizations

LDFLAGS = -L $(HOME)/lib
LIB_MPI = -lgomp 


#======== Libraries ===========


# This is folder of the "main" Makefile ie. the root directory of vlasiatoROOT_FOLDER = $(dir $(abspath $(firstword $(MAKEFILE_LIST))))

# The external libraries are located here
LIBRARY_PREFIX = $(ROOT_FOLDER)external_libs

INC_ZOLTAN = -I$(LIBRARY_PREFIX)/Zoltan/build/include
LIB_ZOLTAN = -L$(LIBRARY_PREFIX)/Zoltan/build/lib -lzoltan

INC_VLSV = -I$(LIBRARY_PREFIX)/vlsv
LIB_VLSV = -L$(LIBRARY_PREFIX)/vlsv -lvlsv

INC_PROFILE = -I$(LIBRARY_PREFIX)/phiprof/include
LIB_PROFILE = -L$(LIBRARY_PREFIX)/phiprof/lib -lphiprof -Wl,-rpath=$(LIBRARY_PREFIX)/phiprof/lib


INC_EIGEN = -isystem ./submodules/eigen/
CXXFLAGS += \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/BUILD_DIR/src/include \
-I/home/LGST/Vlasiator/install_test_1/vlasiator/external_libs/phiprof/include \
-std=c++20
LDFLAGS += -L$(HOME)/LGST/Vlasiator/install_test_1/vlasiator/external_libs/Zoltan/lib
LIBS += -lzoltan

Sincerely,
Eric Comstock