[med-svn] r1391 - in trunk/packages: . clustalw-mpi clustalw-mpi/branches clustalw-mpi/branches/upstream clustalw-mpi/branches/upstream/current

[charles-guest at alioth.debian.org]

Author: charles-guest
Date: 2008-02-16 01:36:44 +0000 (Sat, 16 Feb 2008)
New Revision: 1391

Added:
   trunk/packages/clustalw-mpi/
   trunk/packages/clustalw-mpi/branches/
   trunk/packages/clustalw-mpi/branches/upstream/
   trunk/packages/clustalw-mpi/branches/upstream/current/
   trunk/packages/clustalw-mpi/branches/upstream/current/Makefile
   trunk/packages/clustalw-mpi/tags/
Log:
[svn-inject] Installing original source of clustalw-mpi

Added: trunk/packages/clustalw-mpi/branches/upstream/current/Makefile
===================================================================
--- trunk/packages/clustalw-mpi/branches/upstream/current/Makefile	                        (rev 0)
+++ trunk/packages/clustalw-mpi/branches/upstream/current/Makefile	2008-02-16 01:36:44 UTC (rev 1391)
@@ -0,0 +1,53 @@
+install: clustalw-mpi
+
+clean:
+	/bin/rm -f *.o
+
+OBJECTS = clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o \
+        malign_mpi_pdiff.o util.o trees.o gcgcheck.o \
+	prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o \
+  	calcgapcoeff.o calcprf1.o calcprf2.o calctree.o \
+        readmat.o alnscore.o random.o parallel_compare.o \
+        prfalign.o stupid.o
+
+HEADERS = general.h clustalw.h
+
+CC	= mpicc 
+
+TREES_FLAG = -DSERIAL_NJTREE
+
+#
+# Choose either dynamic or static scheduling for pairalign():
+# the default is to use dynamic scheduling. You might also
+# want to check PAIRALIGN_NCHUNK in clustalw.h. The
+# larger this marco, the smaller the chunk size, default is 100.
+#
+PAIRALIGN_FLAG = -DDYNAMIC_SCHEDULING_PAIRALIGN 
+#PAIRALIGN_FLAG = -DSTATIC_SCHEDULING_PAIRALIGN
+
+CFLAGS  = -c -O3
+#CFLAGS  = -c -O3 -funroll-all-loops
+LFLAGS	= -lm 
+
+clustalw-mpi: $(OBJECTS) 
+	$(CC) -o $@ $(OBJECTS) $(LFLAGS)
+
+interface.o : interface.c $(HEADERS) param.h
+	$(CC) $(CFLAGS) $*.c
+
+readmat.o : readmat.c $(HEADERS) matrices.h
+	$(CC) $(CFLAGS) $*.c
+
+trees.o : trees.c $(HEADERS) dayhoff.h
+	$(CC) $(TREES_FLAG) $(CFLAGS) $*.c
+
+pairalign_new.o : pairalign_new.c $(HEADERS)
+	$(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
+parallel_compare.o : parallel_compare.c $(HEADERS) dayhoff.h
+	$(CC) $(PAIRALIGN_FLAG) $(CFLAGS) $*.c
+
+
+
+.c.o :
+	$(CC) $(CFLAGS) $?
+