Closed broukema closed 6 years ago
broukema
commented
6 years ago Is there an easy way to download the full pull request as either a merge single patch, or else as a series of 22 patch files? I couldn't find any obvious way in the github web interface.
james-s-willis
commented
6 years ago I have merged the master branch into the swift-interface branch so you can just checkout the swift-interface branch. Let me know if that works.
broukema
commented
6 years ago Thanks for the fast response! It looks like this bug is solved (from a naive "does it compile?" point of view), though I get a new compile error. I'll post the new compile error as a separate bug, since I don't know enough to guess if it's related or not.
I won't close this bug because I don't know the code well enough to judge - I'm happy for someone who knows the code better (probably Pascal?) to close it.
broukema
commented
6 years ago OK, from my point of view (compilation), I no longer get any compile errors. My "new" compile
error (previous comment) is because I'm used to using system-level libraries, and the LOCAL.*
definitions in Makefile.config.template made me wonder whether the Makefile favours
native libraries by default. In reality it seems to require hardwiring the native library include
and lib directories (since there's no configure.ac file). I set ADIOSENABLE=off and
HDF_INCL = -I/usr/include/hdf5/serial/
HDF_LIBS = -L/usr/lib/x86_64-linux-gnu/hdf5/serial/and make clean and make compiled fully. There don't seem to be any unit tests
(e.g. make check) for checking the installation.
james-s-willis
commented
6 years ago Yes, I think VELOCIraptor looks locally for the HDF5 library. Therefore, if you want to use a specific version you have to hardcode the path in the Makefile to point to the one you want. What environment are you developing in? Does it have a module system setup? This can help with using specific library versions without hardcoding the library path in the Makefile.
broukema
commented
6 years ago As above: Debian GNU/Linux 4.9.0
dpkg -l |grep hdf5
ii hdf5-helpers 1.10.0-patch1+docs-3+deb9u1 amd64 Hierarchical Data Format 5 (HDF5) - Helper tools
ii libhdf5-100:amd64 1.10.0-patch1+docs-3+deb9u1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-8:amd64 1.8.13+docs-15+deb8u1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-cpp-100:amd64 1.10.0-patch1+docs-3+deb9u1 amd64 Hierarchical Data Format 5 (HDF5) - C++ libraries
ii libhdf5-dev 1.10.0-patch1+docs-3+deb9u1 amd64 Hierarchical Data Format 5 (HDF5) - development files - serial version
ii libhdf5-openmpi-100:amd64 1.10.0-patch1+docs-3+deb9u1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - OpenMPI version
ii libhdf5-serial-dev 1.10.0-patch1+docs-3+deb9u1 all transitional dummy packageThe package libhdf5-8:amd64 looks like an old version which I should probably purge. The files in libhdf5-dev(amd64 architecture) are listed at https://packages.debian.org/stretch/amd64/libhdf5-dev/filelist . There are also libhdf5-openmpi-dev and libhdf5-mpich-dev available (I have libhd5-openmpi-dev installed) - presumably one of these parallel versions would have an advantage over the serial versions for any production level usage. Their files lists are at https://packages.debian.org/stretch/amd64/libhdf5-openmpi-dev/filelist and https://packages.debian.org/stretch/amd64/libhdf5-mpich-dev/filelist .
It looks to me like the hdf5 front-end compiler h5c++ should be used, in analogy to the mpi front-end mpic++. These add include and library options to the default compiler, consistently with the way that the library itself was compiled. It looks like the two cannot be used together, and the -show option for h5c++ is less convenient than the corresponding mpic++ options --showme:compile and --showme:link. However, I'm proposing a pull request https://github.com/pelahi/VELOCIraptor-STF/pull/22 for the Makefile.config.template that works for me using h5c++. This brings me to a separate issue - I haven't yet tested your Makefile.config.SWIFT-template. I'll get back to it soon...
broukema
commented
6 years ago OK, getting back to this bug - your Makefile.config.SWIFT-template works for me, without my needing
to hardwire the hdf5 include and library directories, provided that I apply the following patch against your branch (this includes pull request https://github.com/pelahi/VELOCIraptor-STF/pull/22). I'm showing the patch just for clarity - my guess is that you don't really intend your Makefile.config.SWIFT-template to be added to the master branch, since I don't see any changes that would be needed by a default user.
--- Makefile.config.SWIFT-template 2018-10-22 18:18:40.799523312 +0200
+++ Makefile.config 2018-10-22 18:27:53.723258749 +0200
@@ -5,7 +5,7 @@
#===========================================
#type of system, where libraries are located, etc
#===========================================
-SYSTEM="intel-standard"
+#SYSTEM="intel-standard"
#SYSTEM="gcc-standard"
#SYSTEM="cray"
@@ -14,10 +14,10 @@
#===========================================
#Parallel APIs to turn on
#===========================================
-MPI="off"
+MPI="on"
#reduce impact of MPI memory overhead at the cost of extra cpu cycles, suggested this be turned on
MPIREDUCE="on"
-OMP="off"
+OMP="on"
#===========================================
#===========================================
@@ -25,11 +25,21 @@
#===========================================
LOCALGSL="on"
LOCALFFTW="on"
-LOCALHDF="on"
+LOCALHDF="off"
LOCALADIOS="on"
LOCALXDR="on"
#===========================================
+
+#===========================================
+#native (your operating system) libraries
+#===========================================
+#for using h5c++ -show to find your system level include and library files
+ifneq ($(LOCALHDF),"on")
+ HDFNATIVELIBS="on"
+endif
+#===========================================
+
#===========================================
#Adjust precision
#===========================================
@@ -142,7 +152,7 @@
#alter if necessary to point to local libraries
#===========================================
ifeq ($(LOCALGSL),"on")
- GSL_DIR = /usr/local
+ GSL_DIR =
GSL_INCL = -I$(GSL_DIR)/include/
GSL_LIBS = -L$(GSL_DIR)/lib/
GSL_CONFIG =
@@ -197,8 +207,7 @@
C+ = CC
PARALLEL+=-DUSEMPI
else
- #C+ = mpiCC
- C+ = mpicc
+ C+ = mpic++
MPI_COMPILE_FLAGS = $(shell $(C+) --showme:compile)
MPI_LINK_FLAGS = $(shell $(C+) --showme:link)
PARALLEL+=-DUSEMPI $(MPI_COMPILE_FLAGS)
@@ -331,8 +340,18 @@
ifeq ($(HDFENABLE),"on")
C+FLAGS+= -DUSEHDF
C+LIBS+= -lhdf5_hl_cpp -lhdf5_cpp -lhdf5_hl -lhdf5 -lz -lrt -ldl
- IFLAGS+= $(HDF_INCL)
- LFLAGS+= $(HDF_LIBS)
+ ifeq ($(HDFNATIVELIBS),"on")
+ H5C+ = h5c++
+ # h5c++ (version 1.10.0-patch1+docs-3+deb9u1) does not have
+ # options to show include and library options separately;
+ # awk: $1=$(NF+1) replaces the first field by a null string
+ # and $0 prints the revised string
+ IFLAGS+=$(shell $(H5C+) -show |awk '{$$1=$$(NF+1); print $$0}')
+ LFLAGS+=$(shell $(H5C+) -show |awk '{$$1=$$(NF+1); print $$0}')
+ else
+ IFLAGS+= $(HDF_INCL)
+ LFLAGS+= $(HDF_LIBS)
+ endif
endif
ifeq ($(ADIOSENABLE),"on")
MatthieuSchaller
commented
6 years ago FYI, the SWIFT code is still in heavy development and we can't yet guaranty stability or correct results. At this stage, I'd recommend getting in touch with the team before embarking into a simulation campaign.
PROBLEM:
The variable "mass" on line 226 of
NBodylib/src/NBody/Particle.cxxis not declared (not in that scope, anyway), giving a compile error with gcc-6.3.0 .SYSTEM:
Debian GNU/Linux 4.9.0
dpkg -l |egrep "gcc|autoconf|libtool"
REPRODUCE THE BUG:
Create a directory such as
/tmp/veland git download and compile from scratch:ERROR MESSAGE:
ANALYSIS/HYPOTHESES:
git log --patch NBodylib/src/NBody/Particle.cxxshows that themass*=mscaleline was added on 5 March 2018 with a swift interface update.Should line 78 of Particle.h with
///massbe followed by a line definingmass? Since it seems that swiftsim has masses for all particles, maybe that's what missing? I'm a complete newbie to swift and velociraptor, so I'm just guessing.