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Easyblocks for R extenison patching (including extract) and Extesnion Rm... #435

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merged 5 commits into from Sep 10, 2014
Merged

Easyblocks for R extenison patching (including extract) and Extesnion Rm... #435

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2988a71
Easyblocks for R extenison patching (including extract) and Extesnion…
Jul 8, 2014
76220d2
Update rmpi.py
Aug 1, 2014
ef195ef
Typos and style corrected
Aug 4, 2014
ef787d1
Update rpackage.py
Sep 10, 2014
5351a51
Update rmpi.py
Sep 10, 2014
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12 changes: 9 additions & 3 deletions easybuild/easyblocks/generic/rpackage.py
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Expand Up @@ -112,9 +112,12 @@ def make_cmdline_cmd(self, prefix=None):
else:
prefix = ''

cmd = "R CMD INSTALL %s %s %s %s --no-clean-on-error" % (self.ext_src, confargs, confvars, prefix)
self.log.debug("make_cmdline_cmd returns %s" % cmd)
if self.patches:
cmd = "R CMD INSTALL %s %s %s %s --no-clean-on-error" % (self.ext_dir, confargs, confvars, prefix)
else:
cmd = "R CMD INSTALL %s %s %s %s --no-clean-on-error" % (self.ext_src, confargs, confvars, prefix)
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the cmd value is exactly the same in both cases?!

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Look at more close!
cmd = "R CMD INSTALL %s %s %s %s --no-clean-on-error" % (self.ext_dir, confargs, confvars, prefix)
and
cmd = "R CMD INSTALL %s %s %s %s --no-clean-on-error" % (self.ext_src, confargs, confvars, prefix)

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Maybe split up the command and the tuple then? The cmd string itself is the same?

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Yeah, exactly. Suggestion:

if self.patches:
    loc = self.ext_dir
else:
    loc = self.ext_src
cmd = "R CMD INSTALL %s %s %s %s --no-clean-on-error" % (loc, confargs, confvars, prefix)


self.log.debug("make_cmdline_cmd returns %s" % cmd)
return cmd, None

def extract_step(self):
Expand Down Expand Up @@ -167,7 +170,10 @@ def install_step(self):
def run(self):
"""Install R package as an extension."""

super(RPackage, self).run()
if self.patches:
super(RPackage, self).run(unpack_src=True)
else:
super(RPackage, self).run()

if self.src:
self.ext_src = self.src
Expand Down
8 changes: 7 additions & 1 deletion easybuild/easyblocks/r/rmpi.py
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Expand Up @@ -32,6 +32,7 @@
@author: Toon Willems (Ghent University)
"""
import easybuild.tools.toolchain as toolchain
from distutils.version import LooseVersion
from easybuild.easyblocks.generic.rpackage import RPackage


Expand All @@ -46,12 +47,17 @@ def run(self):
toolchain.MPI_TYPE_MPICH: "MPICH",
#toolchain.MPI_TYPE_LAM: "LAM", # no support for LAM yet
}
# type of MPI
mpi_type = self.toolchain.mpi_family()
Rmpi_type = mpi_types[self.toolchain.MPI_TYPE]
if ((LooseVersion(self.version) >= LooseVersion('0.6-4')) and (mpi_type == toolchain.INTELMPI)):
Rmpi_type = 'INTELMPI'
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this needs a comment... why only since v0.6-4, is it simply not supported in earlier versions?
also mention that MPI_TYPE doesn't distinguish between MPICH and Intel MPI, which is why we also check mpi_family()


self.log.debug("Setting configure args for Rmpi")
self.configureargs = [
"--with-Rmpi-include=%s" % self.toolchain.get_variable('MPI_INC_DIR'),
"--with-Rmpi-libpath=%s" % self.toolchain.get_variable('MPI_LIB_DIR'),
"--with-mpi=%s" % self.toolchain.get_software_root(self.toolchain.MPI_MODULE_NAME)[0],
"--with-Rmpi-type=%s" % mpi_types[self.toolchain.MPI_TYPE],
"--with-Rmpi-type=%s" % Rmpi_type,
]
super(EB_Rmpi, self).run() # it might be needed to get the R cmd and run it with mympirun...