Hello Claudia, as Ian pointed out this can a diffult exercise. What you are encountering is a known bug in our HDF5 interface thorn (https://trac.einsteintoolkit.org/ticket/1851). The ticket does not contain a functioning patch. A solution for your cluster may be to make a symbolic or hard link from H5pubconf-64.h to H5pubconf.h . I do explicitly not suggest this to be a good solution, just something that would allow you work around our bugger HDF5 detection script (and I may call it buggy since I originally wrote that part that breaks). I am fairly sure that renaming the file will break HDF5. A proper fix would be to modify the file arrangements/ExternalLibraries/HDF5/src/detect.sh to look for the correct file (though this will break the script on distributions where the file name differs). I attach a hopefully working patch (untested).
I would typically suggest to look into the directory simfactory/mdb/optionlists and pick one that looks like a good starting point. In your case (depending on how "workstation like" the cluster looks, you may want to start from fedora.cfg which also uses similar file names). The details of what goes into the option list is described here: http://einsteintoolkit.org/documentation/UsersGuide/UsersGuidech6.html#x9-19000B2.1 but please ignore the section on "Compiling with Extra Packages" which outdated (this functionality is in principle still there but will conflict with some newer code in Cactus). You options set F90 and HDF5 seem unusual. When you say passing as arguments to build, exactly what does your command line (and all files mentioned on the command line) look like? Something like: ./simfactory/bin/sim build --optionlist=./my-options and the file my-options contains (leaving out the line numbers): F90=/usr/bin/gfortran F90_OPTIMISE_FLAGS=-O0 HDF5=yes SILENT=no ? Please double (or tripple) check the filename given since simfactory (used to and still may) contain a bug where if an optionlist file is not found it automatically uses the "default" one which is most likely empty in your case (or at least does not set F90). Note that HDF5=yes should no longer be used (the Cactus UserGuide mentions it, but the user guide is out of data and an updated description is in the current git master version of the .tex file [but not yet the .pdf file so you have to use "make UserGuide" to produce the pdf file). Yours, Roland On Wed, 4 May 2016 11:57:17 +0000 Claudia Richoux <[email protected]> wrote: > Hi again, > I'm setting it up on a CoreOS cluster managed with Salt? Any tips for > that, or ideas for what could specifically be causing those errors? > Is there a tutorial for cluster setup? I do have some sysadmin > skills, even though I'm not familiar with cactus. > I'm pretty sure I need to specify the location of the fortran > executable when I build, and I need to somehow get it to figure out > that I have H5pubconf-64.h rather than H5pubconf.h. Would I specify > fortran in the configuration file? Am I doing it wrong? For HDF5, > could I just rename the header file, or would that break stuff? > Thanks, > Claudia > On Wed, 4 May 2016 at 04:02 Ian Hinder <[email protected]> wrote: > > > On 3 May 2016, at 20:03, Claudia Richoux <[email protected]> > > wrote: > > > > Hi Erik, > > I've been following the instructions here: > > https://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users#Compile_Executable > > Specifically, so far, running "./simfactory/bin/sim build > > configfile.config" has been all. > > > > > > Hi Claudia, > > > > Are you following exactly those instructions, including getting a > > Queen Bee account, and building the ET on Queen Bee? That tutorial > > is for Queen Bee only. If you are trying to build the ET on your > > own laptop or workstation, then I recommend what Roland said, which > > is to use the "simplified tutorial for new users". In case you are > > trying to build the ET on a cluster, I should say that setting up > > the ET on a new cluster is quite difficult. > > > > -- > > Ian Hinder > > http://members.aei.mpg.de/ianhin > > > > -- My email is as private as my paper mail. I therefore support encrypting and signing email messages. Get my PGP key from http://keys.gnupg.net.
Index: src/detect.sh
===================================================================
--- src/detect.sh (revision 126)
+++ src/detect.sh (working copy)
@@ -165,9 +165,12 @@
if [ -z "$HDF5_BUILD" -a -n "${HDF5_DIR}" ]; then
# find public include file
for dir in $HDF5_RAW_INC_DIRS; do
- if [ -r "$dir/H5pubconf.h" ]; then
- H5PUBCONF="$H5PUBCONF $dir/H5pubconf.h"
+ for file in H5pubconf.h H5pubconf-64.h H5pubconf-32.h ; do
+ if [ -r "$dir/$file" ]; then
+ H5PUBCONF="$H5PUBCONF $dir/$file"
+ break
fi
+ done
done
if [ -z "$H5PUBCONF" ]; then
echo 'BEGIN ERROR'
smime.p7s
Description: S/MIME cryptographic signature
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