Build on newcomp with clang++. Added .cmd files for newcomp q.

.gitignore

@@ -3,6 +3,7 @@
 /gss
 /main
 /testsurfaces
-/serial.cmd*
+/serial.cmd.[eo]*
+/parallel.cmd.[eo]*
 /save
 */save

Makefile

@@ -3,16 +3,16 @@ BISON = /opt/local/bin/bison
 FLEX = /opt/local/bin/flex
 
 # CXX = g++
-# CXX = mpic++
+CXX = OMPI_CXX=clang++ mpic++ -fno-color-diagnostics --stdlib=libc++ --std=c++11 -I/u/cseed/llvm-3.1/lib/c++/v1
-CXX = clang++ -fno-color-diagnostics --stdlib=libc++ --std=c++11
+# CXX = clang++ -fno-color-diagnostics --stdlib=libc++ --std=c++11
 
 INCLUDES = -I/opt/local/include -I.
 
 # OPTFLAGS = -g
-OPTFLAGS = -O2 -g
+# OPTFLAGS = -O2 -g
-# OPTFLAGS = -O2 -DNDEBUG
+OPTFLAGS = -O2 -DNDEBUG
 
-LDFLAGS = -L/opt/local/lib
+LDFLAGS = -L/opt/local/lib -L/u/cseed/llvm-3.1/lib
 # LDFLAGS = -pg -L/opt/local/lib
 
 CXXFLAGS = $(OPTFLAGS) -Wall -Wno-unused $(INCLUDES)
@@ -95,7 +95,7 @@ parser_files: \
 .PHONY: clean
 clean:
 	rm -f *.o lib/*.o algebra/*.o knot_parser/*.o rd_parser/*.o
-	rm -f main gss
+	rm -f main gss mpimain
 	rm -f gmon.out
 
 .PHONY: realclean

algebra/algebra.cpp

@@ -16,8 +16,8 @@ unsigned_gcd (unsigned a, unsigned b)
 unsigned
 int_gcd (int a, int b)
 {
-  return unsigned_gcd ((unsigned)std::abs (a),
+  return unsigned_gcd ((unsigned)abs (a),
-		       (unsigned)std::abs (b));
+		       (unsigned)abs (b));
 }
 
 uint64
@@ -35,8 +35,8 @@ uint64_gcd (uint64 a, uint64 b)
 uint64
 int64_gcd (int64 a, int64 b)
 {
-  return uint64_gcd ((uint64)std::abs (a),
+  return uint64_gcd ((uint64)abs64 (a),
-		     (uint64)std::abs (b));
+		     (uint64)abs64 (b));
 }
 
 static tuple<unsigned, int, int>
@@ -71,8 +71,8 @@ unsigned_extended_gcd (unsigned a, unsigned b)
 tuple<unsigned, int, int>
 extended_gcd (int a, int b)
 {
-  tuple<unsigned, int, int> t = extended_gcd_1 (std::abs (a),
+  tuple<unsigned, int, int> t = extended_gcd_1 (abs (a),
-						std::abs (b));
+						abs (b));
   unsigned d = get<0> (t);
   int x = get<1> (t),
     y = get<2> (t);
@@ -100,12 +100,12 @@ uint64_lcm (uint64 a, uint64 b)
 
 unsigned int_lcm (int a, int b)
 {
-  return unsigned_lcm ((unsigned)std::abs (a),
+  return unsigned_lcm ((unsigned)abs (a),
-		       (unsigned)std::abs (b));
+		       (unsigned)abs (b));
 }
 
 uint64 int64_lcm (int64 a, int64 b)
 {
-  return uint64_lcm ((uint64)std::abs (a),
+  return uint64_lcm ((uint64)abs64 (a),
-		     (uint64)std::abs (b));
+		     (uint64)abs64 (b));
 }

knot_tables.cpp

@@ -1,7 +1,7 @@
 
 #include <knotkit.h>
 
-#define HOME "/Users/cotton/src/knotkit/"
+#define HOME "/u/cseed/src/knotkit/"
 
 bool verbose = 0;
 
@@ -642,7 +642,7 @@ braid (unsigned n_strands, const basedvector<int, 1> &twists)
     last_twist[i] = 0;
   for (unsigned i = 1; i <= twists.size (); i ++)
     {
-      unsigned t = std::abs (twists[i]);
+      unsigned t = abs (twists[i]);
       last_twist[t] = i;
       last_twist[t + 1] = i;
     }
@@ -657,7 +657,7 @@ braid (unsigned n_strands, const basedvector<int, 1> &twists)
   
   for (unsigned i = 1; i <= twists.size (); i ++)
     {
-      unsigned t = std::abs (twists[i]);
+      unsigned t = abs (twists[i]);
       unsigned e1 = strands[t],
 	e4 = strands[t + 1];
       unsigned e2, e3;

lib/lib.h

@@ -1,5 +1,6 @@
 
 #include <assert.h>
+#include <stdlib.h>
 #include <stdio.h>
 #include <string.h>
 #include <math.h>
@@ -39,6 +40,8 @@ typedef unsigned long ulong;
 typedef long long int64;
 typedef unsigned long long uint64;
 
+inline int64 abs64 (int64 x) { return llabs (x); }
+
 typedef size_t hash_t;
 
 static const unsigned uint8_bits = 8;

main.cpp

@@ -692,12 +692,53 @@ test_knot_sq ()
     }
 }
 
+pair<mod_map<Z2>, mod_map<Z2> > 
+compute_kh_sq (const knot_desc &desc)
+{
+}
+
 int
 main ()
 {
+#if 1
+  knot_desc desc;
+  desc.t = knot_desc::HTW;
+  desc.i = 15;
+  desc.j = 15020;
+  
+  char buf[1000];
+  sprintf (buf, "/scratch/network/cseed/incoming/K%d_%d.dat.gz",
+	   desc.i, desc.j);
+  
+  desc = knot_desc (knot_desc::ROLFSEN, 3, 1);
+
+  knot_diagram kd = desc.diagram ();
+
+  cube<Z2> c (kd);
+  mod_map<Z2> d = c.compute_d (1, 0, 0, 0, 0);
+  
+  chain_complex_simplifier<Z2> s (c.khC, d, 1);
+  assert (s.new_d == 0);
+  
+  steenrod_square sq (c, d, s);
+  mod_map<Z2> sq1 = sq.sq1 ();
+  mod_map<Z2> sq2 = sq.sq2 ();
+  
+  assert (sq1.compose (sq1) == 0);
+  assert (sq2.compose (sq2) + sq1.compose (sq2).compose (sq1) == 0);
+
+#if 1
+  {
+    file_writer w (buf);
+    write (w, sq1);
+    write (w, sq2);
+  }
+#endif
+#endif
+  return 0;
+  
   // convert_knot_sq ();
   test_knot_sq ();
-  return 0;
   
   // test_sage_show ();
   dump_sage ();

mpimain.cpp

@@ -87,32 +87,6 @@ master ()
     }
 }
 
-pair<mod_map<Z2>, mod_map<Z2> > 
-compute_kh_sq (const knot_desc &desc)
-{
-  knot_diagram kd = desc.diagram ();
-  
-  unsigned rank = self_rank ();
-  
-  printf ("[% 2d] %s\n", rank, kd.name.c_str ());
-  fflush (stdout);
-  
-  cube<Z2> c (kd);
-  mod_map<Z2> d = c.compute_d (1, 0, 0, 0, 0);
-  
-  chain_complex_simplifier<Z2> s (c.khC, d, 1);
-  assert (s.new_d == 0);
-  
-  steenrod_square sq (c, d, s);
-  mod_map<Z2> sq1 = sq.sq1 ();
-  mod_map<Z2> sq2 = sq.sq2 ();
-  
-  assert (sq1.compose (sq1) == 0);
-  assert (sq2.compose (sq2) + sq1.compose (sq2).compose (sq1) == 0);
-
-  return pair<mod_map<Z2>, mod_map<Z2> > (sq1, sq2);
-}
-
 void
 slave ()
 {
@@ -127,21 +101,35 @@ slave ()
 	  {
 	    knot_desc desc;
 	    desc.t = (knot_desc::table)recv_int ();
-	    desc.i = (knot_desc::table)recv_int ();
+	    desc.i = (unsigned)recv_int ();
-	    desc.j = (knot_desc::table)recv_int ();
+	    desc.j = (unsigned)recv_int ();
 	    
 	    printf ("[% 2d] CMD_DO %s\n", rank, desc.name ().c_str ());
 	    
 	    char buf[1000];
-	    sprintf (buf, "incoming/K%d_%d.dat", desc.i, desc.j);
+	    sprintf (buf, "/scratch/network/cseed/incoming/K%d_%d.dat.gz",
+		     desc.i, desc.j);
 	    
-	    pair<mod_map<Z2>, mod_map<Z2> > p = compute_kh_sq (knot_kh_sq, desc);
+	    // desc = knot_desc (knot_desc::ROLFSEN, 3, 1);
 	    
-	    {
+	    knot_diagram kd = desc.diagram ();
-	      writer w (buf);
+	    
-	      write (w, p.first);
+	    cube<Z2> c (kd);
-	      write (w, p.second);
+	    mod_map<Z2> d = c.compute_d (1, 0, 0, 0, 0);
-	    }
+	    
+	    chain_complex_simplifier<Z2> s (c.khC, d, 1);
+	    assert (s.new_d == 0);
+	    
+	    steenrod_square sq (c, d, s);
+	    mod_map<Z2> sq1 = sq.sq1 ();
+	    mod_map<Z2> sq2 = sq.sq2 ();
+	    
+	    assert (sq1.compose (sq1) == 0);
+	    assert (sq2.compose (sq2) + sq1.compose (sq2).compose (sq1) == 0);
+	    
+	    file_writer w (buf);
+	    write (w, sq1);
+	    write (w, sq2);
 	    
 	    send_int (0, 0);
 	  }

parallel.cmd

@@ -0,0 +1,20 @@
+# mpi job, runtime max 5days
+#PBS -l nodes=2:ppn=6,walltime=96:00:00
+# xxx PBS -l mem=80gb
+#
+# sends mail if the process aborts, when it begins, and
+# when it ends (abe)
+#PBS -m abe
+#
+module load openmpi/gcc
+# go to the directory with the program
+cd $HOME/src/knotkit
+
+LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/u/cseed/llvm-3.1/lib
+export LD_LIBRARY_PATH
+
+echo $LD_LIBRARY_PATH
+
+# and run it
+numprocs=`wc -l <${PBS_NODEFILE}`
+mpiexec -np $numprocs ./mpimain

serial.cmd

@@ -0,0 +1,15 @@
+# serial job
+#PBS -l nodes=1:ppn=1,walltime=96:00:00
+# xxx PBS -l mem=80gb
+#
+# sends mail if the process aborts, when it begins, and
+# when it ends (abe)
+#PBS -m abe
+#
+# load intel compiler settings before running the program
+# since we compiled it with intel 10.1
+# module load intel/10.1
+# go to the directory with the program
+cd $HOME/src/knotkit
+# and run it
+./main