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eic_tools
Spack
Commits
46726180
Commit
46726180
authored
5 years ago
by
Massimiliano Culpo
Committed by
Adam J. Stewart
5 years ago
Browse files
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raxml: simplified recipe by removing SIMD variants (#12952)
Now the support for SSE3 or AVX is tested on the selected target
parent
c065c25a
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1 changed file
var/spack/repos/builtin/packages/raxml/package.py
+12
-46
12 additions, 46 deletions
var/spack/repos/builtin/packages/raxml/package.py
with
12 additions
and
46 deletions
var/spack/repos/builtin/packages/raxml/package.py
+
12
−
46
View file @
46726180
...
@@ -2,26 +2,22 @@
...
@@ -2,26 +2,22 @@
# Spack Project Developers. See the top-level COPYRIGHT file for details.
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from
spack
import
*
from
spack.spec
import
ConflictsInSpecError
import
glob
import
glob
class
Raxml
(
Package
):
class
Raxml
(
Package
):
"""
RAxML (Randomized Axelerated Maximum Likelihood) is a program for
"""
RAxML (Randomized Axelerated Maximum Likelihood) is a program for
sequential and parallel Maximum Likelihood based inference of large
sequential and parallel Maximum Likelihood based inference of large
phylogenetic trees.
"""
phylogenetic trees.
"""
homepage
=
"
https://sco.h-its.org/exelixis/web/software/raxml
"
homepage
=
"
https://sco.h-its.org/exelixis/web/software/raxml
"
url
=
"
https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz
"
url
=
"
https://github.com/stamatak/standard-RAxML/archive/v8.2.11.tar.gz
"
version
(
'
8.2.11
'
,
'
6bd5c4e1f93003ccf13c9b59a5d080ab
'
)
version
(
'
8.2.11
'
,
'
6bd5c4e1f93003ccf13c9b59a5d080ab
'
)
variant
(
'
mpi
'
,
default
=
True
,
description
=
'
Enable MPI parallel support
'
)
variant
(
'
mpi
'
,
default
=
True
,
description
=
'
Enable MPI parallel support
'
)
variant
(
'
pthreads
'
,
default
=
False
,
description
=
'
Enable pthreads version
'
)
variant
(
'
pthreads
'
,
default
=
False
,
description
=
'
Enable pthreads version
'
)
variant
(
'
sse
'
,
default
=
False
,
description
=
'
Enable SSE in order to substantially speed up execution
'
)
variant
(
'
avx
'
,
default
=
False
,
description
=
'
Enable AVX in order to substantially speed up execution
'
)
depends_on
(
'
mpi
'
,
when
=
'
+mpi
'
)
depends_on
(
'
mpi
'
,
when
=
'
+mpi
'
)
...
@@ -38,36 +34,6 @@ class Raxml(Package):
...
@@ -38,36 +34,6 @@ class Raxml(Package):
# can't build multiple binaries in parallel without things breaking
# can't build multiple binaries in parallel without things breaking
parallel
=
False
parallel
=
False
def
flag_handler
(
self
,
name
,
flags
):
arch
=
''
spec
=
self
.
spec
if
spec
.
satisfies
(
"
platform=cray
"
):
# FIXME; It is assumed that cray is x86_64.
# If you support arm on cray, you need to fix it.
arch
=
'
x86_64
'
if
arch
!=
'
x86_64
'
and
not
spec
.
target
.
family
==
'
x86_64
'
:
if
spec
.
satisfies
(
"
+sse
"
):
raise
ConflictsInSpecError
(
spec
,
[(
spec
,
spec
.
architecture
.
target
,
spec
.
variants
[
'
sse
'
],
'
+sse is valid only on x86_64
'
)]
)
if
spec
.
satisfies
(
"
+avx
"
):
raise
ConflictsInSpecError
(
spec
,
[(
spec
,
spec
.
architecture
.
target
,
spec
.
variants
[
'
avx
'
],
'
+avx is valid only on x86_64
'
)]
)
return
(
flags
,
None
,
None
)
def
install
(
self
,
spec
,
prefix
):
def
install
(
self
,
spec
,
prefix
):
mkdirp
(
prefix
.
bin
)
mkdirp
(
prefix
.
bin
)
files
=
glob
.
iglob
(
"
Makefile.*
"
)
files
=
glob
.
iglob
(
"
Makefile.*
"
)
...
@@ -78,11 +44,11 @@ def install(self, spec, prefix):
...
@@ -78,11 +44,11 @@ def install(self, spec, prefix):
makefile
.
filter
(
'
mpicc
'
,
self
.
spec
[
'
mpi
'
].
mpicc
)
makefile
.
filter
(
'
mpicc
'
,
self
.
spec
[
'
mpi
'
].
mpicc
)
if
spec
.
target
.
family
==
'
x86_64
'
:
if
spec
.
target
.
family
==
'
x86_64
'
:
if
spec
.
satisfies
(
'
+mpi
+avx
+pthreads
'
):
if
spec
.
satisfies
(
'
+mpi +pthreads
'
)
and
'
avx
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.AVX.HYBRID.gcc
'
)
make
(
'
-f
'
,
'
Makefile.AVX.HYBRID.gcc
'
)
install
(
'
raxmlHPC-HYBRID-AVX
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-HYBRID-AVX
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+mpi
+sse
+pthreads
'
):
if
spec
.
satisfies
(
'
+mpi +pthreads
'
)
and
'
sse3
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.SSE3.HYBRID.gcc
'
)
make
(
'
-f
'
,
'
Makefile.SSE3.HYBRID.gcc
'
)
install
(
'
raxmlHPC-HYBRID-SSE3
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-HYBRID-SSE3
'
,
prefix
.
bin
)
...
@@ -90,11 +56,11 @@ def install(self, spec, prefix):
...
@@ -90,11 +56,11 @@ def install(self, spec, prefix):
make
(
'
-f
'
,
'
Makefile.HYBRID.gcc
'
)
make
(
'
-f
'
,
'
Makefile.HYBRID.gcc
'
)
install
(
'
raxmlHPC-HYBRID
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-HYBRID
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+mpi
+avx
'
)
:
if
spec
.
satisfies
(
'
+mpi
'
)
and
'
avx
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.AVX.MPI.gcc
'
)
make
(
'
-f
'
,
'
Makefile.AVX.MPI.gcc
'
)
install
(
'
raxmlHPC-MPI-AVX
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-MPI-AVX
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+mpi
+sse
'
)
:
if
spec
.
satisfies
(
'
+mpi
'
)
and
'
sse3
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.SSE3.MPI.gcc
'
)
make
(
'
-f
'
,
'
Makefile.SSE3.MPI.gcc
'
)
install
(
'
raxmlHPC-MPI-SSE3
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-MPI-SSE3
'
,
prefix
.
bin
)
...
@@ -102,11 +68,11 @@ def install(self, spec, prefix):
...
@@ -102,11 +68,11 @@ def install(self, spec, prefix):
make
(
'
-f
'
,
'
Makefile.MPI.gcc
'
)
make
(
'
-f
'
,
'
Makefile.MPI.gcc
'
)
install
(
'
raxmlHPC-MPI
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-MPI
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+pthreads
+avx
'
)
:
if
spec
.
satisfies
(
'
+pthreads
'
)
and
'
avx
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.AVX.PTHREADS.gcc
'
)
make
(
'
-f
'
,
'
Makefile.AVX.PTHREADS.gcc
'
)
install
(
'
raxmlHPC-PTHREADS-AVX
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-PTHREADS-AVX
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+pthreads
+sse
'
)
:
if
spec
.
satisfies
(
'
+pthreads
'
)
and
'
sse3
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.SSE3.PTHREADS.gcc
'
)
make
(
'
-f
'
,
'
Makefile.SSE3.PTHREADS.gcc
'
)
install
(
'
raxmlHPC-PTHREADS-SSE3
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-PTHREADS-SSE3
'
,
prefix
.
bin
)
...
@@ -114,11 +80,11 @@ def install(self, spec, prefix):
...
@@ -114,11 +80,11 @@ def install(self, spec, prefix):
make
(
'
-f
'
,
'
Makefile.PTHREADS.gcc
'
)
make
(
'
-f
'
,
'
Makefile.PTHREADS.gcc
'
)
install
(
'
raxmlHPC-PTHREADS
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-PTHREADS
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+sse
'
)
:
if
'
sse3
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.SSE3.gcc
'
)
make
(
'
-f
'
,
'
Makefile.SSE3.gcc
'
)
install
(
'
raxmlHPC-SSE3
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-SSE3
'
,
prefix
.
bin
)
if
spec
.
satisfies
(
'
+avx
'
)
:
if
'
avx
'
in
spec
.
target
:
make
(
'
-f
'
,
'
Makefile.AVX.gcc
'
)
make
(
'
-f
'
,
'
Makefile.AVX.gcc
'
)
install
(
'
raxmlHPC-AVX
'
,
prefix
.
bin
)
install
(
'
raxmlHPC-AVX
'
,
prefix
.
bin
)
...
...
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