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| .. | | 03-May-2022 | - |
| applications/ | H | 07-May-2005 | - | 24,451 | 16,914 |
| autom4te.cache/ | H | 07-May-2005 | - | 39,208 | 36,288 |
| compilerTests/ | H | 07-May-2005 | - | 230 | 163 |
| doc/ | H | 07-May-2005 | - | 7,198 | 6,040 |
| examples/ | H | 07-May-2005 | - | 52,389 | 50,840 |
| framework/ | H | 07-May-2005 | - | 61,916 | 43,199 |
| tools/ | H | 07-May-2005 | - | 1,771 | 1,364 |
| AUTHORS | H A D | 07-May-2005 | 526 | 29 | 24 |
| Coulomb.vcproj | H A D | 07-May-2005 | 43.3 KiB | 1,546 | 1,545 |
| Dcd2dcd.vcproj | H A D | 07-May-2005 | 13.9 KiB | 538 | 537 |
| FAQ.compiler | H A D | 07-May-2005 | 1.3 KiB | 39 | 25 |
| HOWTODO | H A D | 07-May-2005 | 533 | 19 | 12 |
| LICENSE | H A D | 07-May-2005 | 33.8 KiB | 602 | 530 |
| Makefile.am | H A D | 07-May-2005 | 225 | 11 | 2 |
| Makefile.depend | H A D | 07-May-2005 | 1.4 KiB | 38 | 17 |
| Makefile.in | H A D | 07-May-2005 | 13.9 KiB | 461 | 373 |
| Protomol.sln | H A D | 07-May-2005 | 1.7 KiB | 36 | 35 |
| Protomol.vcproj | H A D | 07-May-2005 | 45.6 KiB | 1,630 | 1,629 |
| README | H A D | 07-May-2005 | 8.8 KiB | 210 | 148 |
| TODOLIST | H A D | 07-May-2005 | 1.5 KiB | 48 | 27 |
| aclocal.m4 | H A D | 07-May-2005 | 30.1 KiB | 837 | 703 |
| compile_with_aix_xlc_debug.ll | H A D | 07-May-2005 | 583 | 32 | 6 |
| compile_with_aix_xlc_mpi.ll | H A D | 07-May-2005 | 598 | 32 | 6 |
| compilerVersion.pl | H A D | 07-May-2005 | 493 | 27 | 25 |
| configure | H A D | 07-May-2005 | 542.1 KiB | 19,429 | 16,799 |
| configure.in | H A D | 07-May-2005 | 37.8 KiB | 1,243 | 1,101 |
| install-sh | H A D | 07-May-2005 | 5.4 KiB | 252 | 153 |
| missing | H A D | 07-May-2005 | 10 KiB | 337 | 263 |
| mkinstalldirs | H A D | 07-May-2005 | 1.8 KiB | 100 | 72 |
| protomol_config.h.in | H A D | 07-May-2005 | 4.5 KiB | 184 | 123 |
| protomol_config_windows.cpp | H A D | 07-May-2005 | 86 | 7 | 5 |
| protomol_config_windows.h | H A D | 07-May-2005 | 1.3 KiB | 47 | 19 |
| realclean | H A D | 07-May-2005 | 994 | 23 | 11 |
| realmake | H A D | 07-May-2005 | 154 | 5 | 2 |
| tags | H A D | 07-May-2005 | 971.1 KiB | 7,486 | 7,485 |
README
1 HOWTO install ProtoMol
2------------------------
3
4
5 USER INSTRUCTIONS
6-------------------
7
80) If your autoconf version is less than 2.52 (autoconf --version) run first:
9
10 aclocal; autoheader; automake -a
11
121) Run one configure script for your platform:
13
14 ./configure # tries to find best preset
15 ./configure --with-aix-xlc # xlC for AIX with optimization flags
16 ./configure --with-aix-xlc-mpi # xlC for AIX with MPI and optimization flags
17 ./configure --with-gcc # g++ for generic with optimization flags
18 ./configure --with-gcc-debug # g++ for generic with debugging flags
19 ./configure --with-gcc-mpich # g++ for generic with MPICH flags
20 ./configure --with-hpux-cc # aCC for HPUX optimization flags
21 ./configure --with-hpux-cc-mpi # aCC for HPUX with MPI and optimization flags
22 ./configure --with-icc # icc for generic with optimization flags
23 ./configure --with-icc-mpich # icc for generic with MPICH and optimization flags
24 ./configure --with-icc-mpich-debug # icc for generic with MPICH and debugging flags
25 ./configure --with-irix-mipspro # CC for IRIX with optimization flags
26 ./configure --with-irix-mipspro-mpi # CC for IRIX with MPI and optimization flags
27 ./configure --with-ppc-xlc # xlC for PPC with optimization flags
28 ./configure --with-sun-gcc # g++ for SUN with optimization flags
29
302) Run depend target to generate dependencies and compile the framework:
31
32 make depend; make
33
34
35
36 DEVELOPER INSTRUCTIONS
37------------------------
38
390) If your autoconf version is less than 2.52 (autoconf --version) run first:
40
41 aclocal; autoheader; automake -a
42
431) Run one configure script for your platform:
44
45 ./configure --with-aix-xlc xlC for AIX with optimization flags
46 ./configure --with-aix-xlc-debug xlC for AIX with debugging flags
47 ./configure --with-aix-xlc-mpi xlC for AIX with MPI and optimization flags
48 ./configure --with-aix-xlc-mpi-debug xlC for AIX with MPI and debugging flags
49 ./configure --with-gcc g++ for generic with optimization flags
50 ./configure --with-gcc-debug g++ for generic with debugging flags
51 ./configure --with-gcc-debug-gdb g++ for generic with debugging and gdb flags
52 ./configure --with-gcc-mpich g++ for generic with MPICH flags
53 ./configure --with-gcc-mpich-debug g++ for generic with MPICH debug flags
54 ./configure --with-gcc-mpich-xeon g++ for generic with MPICH xeon flags
55 ./configure --with-hpux-cc aCC for HPUX optimization flags
56 ./configure --with-hpux-cc-debug aCC for HPUX with debugging flags
57 ./configure --with-hpux-cc-mpi aCC for HPUX with MPI and optimization flags
58 ./configure --with-hpux-cc-mpi-debug aCC for HPUX with MPI and debugging flags
59 ./configure --with-icc icc for generic with optimization flags
60 ./configure --with-icc-debug icc for generic with debugging flags
61 ./configure --with-icc-mpich icc for generic with MPICH and optimization flags
62 ./configure --with-icc-mpich-xeon icc for generic with MPICH and optimization flags
63 ./configure --with-icc-mpich-debug icc for generic with MPICH and debugging flags
64 ./configure --with-irix-mipspro CC for IRIX with optimization flags
65 ./configure --with-irix-mipspro-debug CC for IRIX with debugging flags
66 ./configure --with-irix-mipspro-mpi CC for IRIX with MPI and optimization flags
67 ./configure --with-irix-mipspro-mpi-debug CC for IRIX with MPI and debugging flags
68 ./configure --with-ppc-xlc xlC for PPC with optimization flags
69 ./configure --with-pcc-xlc-debug xlC for PPC with debugging flags
70 ./configure --with-sun-gcc g++ for SUN with optimization flags
71
72 We recommend for testing purpose to use debugging since it takes less time to compile.
73
74
752) Run depend target to generate dependencies and compile the framework:
76
77 make clean; make depend; make
78
79 We recommend to do a "make clean" since the dependencies are not always
80 correctly encountered.
81
82
83 Adding new files to the framework or the applications
84-------------------------------------------------------
85
861) Add your new files to the Makefile.am in the same directory
87
882) Generate the new configure file:
89
90 autoreconf -f -i --verbose
91
92 or
93
94 ./realmake <arguments> # cleans up all and runs autoconf
95
96 or
97
98 aclocal; autoheader; autoconf; automake -a # if you do not have autoconf >= V2.53
99
100
101 Adding new Makefile directories
102------------------------
1031) You have to add your new Makefile filename relative to
104 the root of protomol into configure.ac (at the end of the file),
105 and the directory name parent to it.
106
1072) Generate the new configure file as under addinf files.
108
109
110 HOWTO set compiler flags
111--------------------------
112 This can be done if you don't want to use the --with-platform-cxx configure
113 options
114
115 Set CXX environment variable to the compiler you want to use
116 (e.g. setenv CXX g++)
117
118 Set CXXFLAGS environment variable to the compiler flags you want to use
119 (e.g. setenv CXXFLAGS "-O3")
120
121 For more detailed informations:
122 ./configure --help
123
124
125 Compiler troubles
126-------------------
127 If the check of your compiler(s) fails try another configurations or you may
128 change/remove some compiler flags or libraries in ./configure.ac. If you have
129 still have troubles to compile or run automake/autoconf take look at FAQ.compiler.
130
131 If you have troubles to link/compile with external libraries you may look at
132 test programs in compilerTests to figure out the compiler/library flags.
133
134
135 Autoconf troubles / older versions
136------------------------------------
137 configure.ac expects autoconf version 2.53 or higher, in order generate makefiles
138 with older autoconf versions edit configure.ac and comment out what is below
139 Autoconf 2.53 and uncomment below Autoconf 2.13 and copy configure.ac to configure.in
140 You may also use a symbolic link to configure.in and use:
141 aclocal; autoheader; autoconf; automake -a
142
143 64-bit
144--------
145 ProtoMol supports compilation of 32-bit and 64-bit. On AIX you change to 64 with:
146 setenv OBJECT_MODE 64
147
148
149 PNG
150-----
151 The io library supports a PNG writer, but also PPM.
152
153
154 GLUT
155------
156 GLUT is a tool library to simplify OpenGL usage.
157
158
159 FFT
160-----
161 ProtoMol supports different FFT interfaces: FFTW (version 3 and 2), ESSL (AIX), complib.sgimath (IRIX).
162 You can specify your FFT of choice by --with-fft=[sgi|essl|fftw2|fftw3|zfft].
163 Use '--with-fftw3=<path>' to specify install path of FFTW, ESSL and complib.sgimath are assumed to
164 be at default locations. If you do not have any of these FFT libraries, ZFFT is used by default,
165 which is a subsitute for complib.sgimath. Note that ZFFT does not support all kind of numbers.
166 Note that ESSL's FFT does not handle all kind of numbers. ESSL aborts with the error message
167 "DCFT3 : 2538-2030 The transform length (ARG NO. 7, 8 or 9)", where 7 stands for the z-dim,
168 8 the y-dim and 9 the x-dim.
169 http:://www.fftw.org
170
171
172 Timing
173--------
174 wall : totale time, incl. initialization & IO
175 run : running the simulation for n steps, incl. output
176 integration : running the simulation for n steps, excl. output
177 forces : evaluating the forces, excl. communication
178 com : sending and recieving data
179 idle : waiting for the master to send next work package and waiting for barrieres
180
181
182 Parallel
183----------
184 useBarrier : boolean =false : if MPI_Barrier should be called before global communication
185 parallelMode : string : static, dynamic or masterSlave
186 =static : static load balancing, no com. between master and slaves, only slaves
187 =dynamic : master-slave, where the master does some work in-between,
188 parallelPipe should be accordingly set
189 masterSlave : pure master-slave, where the master serves the slaves
190 maxPackages : int : max. number of work packages per node per force; increased
191 packages, better load balance, but more communication
192 parallelPipe : int : pipe size of packages send to each slave; increased pipe less idle
193 slaves, but less load balancing
194
195
196
197 NOTES
198-------
199 Don't worry if it's taking a long time to compile ...
200
201 To clean the whole package:
202
203 ./realclean
204
205
206
207 Contact Information
208---------------------
209 protomol@cse.nd.edu.
210