[gmx-users] problem about compiling mdrun_mpi under cygwin

[Xiang Mao]

Hi, there:
     I met a problem when I try to compile mdrun_mpi using configure
--enable-mpi, I have mpich2 installed. I got some error message like the
following(sorry, it is too long, hope you do not mind). I am wondering if
anyone could tell me how to deal with it. Thank you so much.

Best wishes,
mao

mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops    mdrun.c   -o mdrun
mdrun.c:40:22: typedefs.h: No such file or directory
mdrun.c:41:20: macros.h: No such file or directory
mdrun.c:42:22: copyrite.h: No such file or directory
mdrun.c:43:18: main.h: No such file or directory
mdrun.c:44:22: statutil.h: No such file or directory
mdrun.c:45:21: smalloc.h: No such file or directory
mdrun.c:46:19: futil.h: No such file or directory
mdrun.c:48:19: edsam.h: No such file or directory
mdrun.c:49:19: mdrun.h: No such file or directory
In file included from mdrun.c:50:
xmdrun.h:46:21: network.h: No such file or directory
xmdrun.h:47:20: tgroup.h: No such file or directory
xmdrun.h:48:20: filenm.h: No such file or directory
xmdrun.h:49:20: mshift.h: No such file or directory
xmdrun.h:50:19: force.h: No such file or directory
xmdrun.h:53:20: mdebin.h: No such file or directory
xmdrun.h:54:17: vcm.h: No such file or directory
xmdrun.h:55:19: vsite.h: No such file or directory
xmdrun.h:56:27: gmx_wallcycle.h: No such file or directory
In file included from mdrun.c:50:
xmdrun.h:72: error: parse error before "bool"
xmdrun.h:72: warning: no semicolon at end of struct or union
xmdrun.h:73: warning: type defaults to `int' in declaration of `c6'
xmdrun.h:73: warning: type defaults to `int' in declaration of `c12'
xmdrun.h:73: warning: data definition has no type or storage class
xmdrun.h:74: error: parse error before "xi_6"
xmdrun.h:74: warning: type defaults to `int' in declaration of `xi_6'
xmdrun.h:74: warning: type defaults to `int' in declaration of `xi_12'
xmdrun.h:74: warning: data definition has no type or storage class
xmdrun.h:75: error: parse error before '}' token
xmdrun.h:75: warning: type defaults to `int' in declaration of `t_coupl_LJ'
xmdrun.h:75: warning: data definition has no type or storage class
xmdrun.h:80: error: parse error before "bool"
xmdrun.h:80: warning: no semicolon at end of struct or union
xmdrun.h:81: warning: type defaults to `int' in declaration of `a'
xmdrun.h:81: warning: type defaults to `int' in declaration of `b'
xmdrun.h:81: warning: type defaults to `int' in declaration of `c'
xmdrun.h:81: warning: data definition has no type or storage class
xmdrun.h:82: error: parse error before "xi_a"
xmdrun.h:82: warning: type defaults to `int' in declaration of `xi_a'
xmdrun.h:82: warning: type defaults to `int' in declaration of `xi_b'
xmdrun.h:82: warning: type defaults to `int' in declaration of `xi_c'
xmdrun.h:82: warning: data definition has no type or storage class
xmdrun.h:83: error: parse error before '}' token
xmdrun.h:83: warning: type defaults to `int' in declaration of `t_coupl_BU'
xmdrun.h:83: warning: data definition has no type or storage class
xmdrun.h:88: error: parse error before "bool"
xmdrun.h:88: warning: no semicolon at end of struct or union
xmdrun.h:89: warning: type defaults to `int' in declaration of `Q'
xmdrun.h:89: warning: data definition has no type or storage class
xmdrun.h:90: error: parse error before "xi_Q"
xmdrun.h:90: warning: type defaults to `int' in declaration of `xi_Q'
xmdrun.h:90: warning: data definition has no type or storage class
xmdrun.h:91: warning: type defaults to `int' in declaration of `t_coupl_Q'
xmdrun.h:91: warning: data definition has no type or storage class
xmdrun.h:96: error: parse error before "t_iparams"
xmdrun.h:96: warning: no semicolon at end of struct or union
xmdrun.h:97: warning: type defaults to `int' in declaration of `iprint'
xmdrun.h:97: warning: data definition has no type or storage class
xmdrun.h:98: warning: type defaults to `int' in declaration of
`t_coupl_iparams'
xmdrun.h:98: warning: data definition has no type or storage class
xmdrun.h:101: error: parse error before "real"
xmdrun.h:101: warning: no semicolon at end of struct or union
xmdrun.h:102: warning: type defaults to `int' in declaration of `av_value'
xmdrun.h:102: warning: data definition has no type or storage class
xmdrun.h:103: error: parse error before "ref_value"
xmdrun.h:103: warning: type defaults to `int' in declaration of `ref_value'
xmdrun.h:103: warning: data definition has no type or storage class
xmdrun.h:104: error: parse error before "bObsUsed"
xmdrun.h:104: warning: type defaults to `int' in declaration of `bObsUsed'
xmdrun.h:104: warning: data definition has no type or storage class
xmdrun.h:106: error: parse error before '*' token
xmdrun.h:106: warning: type defaults to `int' in declaration of `tcLJ'
xmdrun.h:106: warning: data definition has no type or storage class
xmdrun.h:107: error: parse error before '*' token
xmdrun.h:107: warning: type defaults to `int' in declaration of `tcBU'
xmdrun.h:107: warning: data definition has no type or storage class
xmdrun.h:108: error: parse error before '*' token
xmdrun.h:108: warning: type defaults to `int' in declaration of `tcQ'
xmdrun.h:108: warning: data definition has no type or storage class
xmdrun.h:109: error: parse error before '*' token
xmdrun.h:109: warning: type defaults to `int' in declaration of `tIP'
xmdrun.h:109: warning: data definition has no type or storage class
xmdrun.h:111: error: parse error before "bInter"
xmdrun.h:111: warning: type defaults to `int' in declaration of `bInter'
xmdrun.h:111: warning: data definition has no type or storage class
xmdrun.h:112: error: parse error before "bVirial"
xmdrun.h:112: warning: type defaults to `int' in declaration of `bVirial'
xmdrun.h:112: warning: data definition has no type or storage class
xmdrun.h:114: error: parse error before '}' token
xmdrun.h:114: warning: type defaults to `int' in declaration of
`t_coupl_rec'
xmdrun.h:114: warning: data definition has no type or storage class
xmdrun.h:116: error: parse error before "t_coupl_rec"
xmdrun.h:118: error: parse error before "t_coupl_rec"
xmdrun.h:120: error: parse error before "t_commrec"
xmdrun.h:122: error: parse error before '*' token
xmdrun.h:125: error: parse error before '*' token
xmdrun.h:125: error: parse error before "t_filenm"
xmdrun.h:127: warning: type defaults to `int' in declaration of
`init_coupling'
xmdrun.h:127: warning: data definition has no type or storage class
xmdrun.h:129: error: parse error before "rvec"
xmdrun.h:131: error: parse error before "real"
xmdrun.h:134: error: parse error before "t_filenm"
xmdrun.h:143: error: parse error before "rvec"
xmdrun.h:147: error: parse error before "mol_dipole"
xmdrun.h:147: error: parse error before "rvec"
xmdrun.h:147: warning: type defaults to `int' in declaration of `mol_dipole'
xmdrun.h:147: warning: data definition has no type or storage class
xmdrun.h:150: error: parse error before "calc_mu_aver"
xmdrun.h:150: error: parse error before '*' token
xmdrun.h:151: warning: type defaults to `int' in declaration of
`calc_mu_aver'
xmdrun.h:151: warning: data definition has no type or storage class
xmdrun.h:157: error: parse error before "real"
xmdrun.h:157: warning: no semicolon at end of struct or union
xmdrun.h:159: error: parse error before "bComb"
xmdrun.h:159: warning: type defaults to `int' in declaration of `bComb'
xmdrun.h:159: warning: type defaults to `int' in declaration of `bVerbose'
xmdrun.h:159: warning: type defaults to `int' in declaration of `bLogEps'
xmdrun.h:159: warning: data definition has no type or storage class
xmdrun.h:160: error: parse error before '}' token
xmdrun.h:160: warning: type defaults to `int' in declaration of `t_ffscan'
xmdrun.h:160: warning: data definition has no type or storage class
xmdrun.h:163: error: parse error before "update_forcefield"
xmdrun.h:164: error: parse error before "t_filenm"
xmdrun.h:165: warning: type defaults to `int' in declaration of
`update_forcefield'
xmdrun.h:165: warning: data definition has no type or storage class
xmdrun.h:168: error: parse error before "print_forcefield"
xmdrun.h:168: error: parse error before "real"
xmdrun.h:170: warning: type defaults to `int' in declaration of
`print_forcefield'
xmdrun.h:170: warning: data definition has no type or storage class
xmdrun.h:173: error: parse error before '*' token
mdrun.c:51:24: checkpoint.h: No such file or directory
mdrun.c:54:18: pull.h: No such file or directory
mdrun.c: In function `main':
mdrun.c:251: error: `t_commrec' undeclared (first use in this function)
mdrun.c:251: error: (Each undeclared identifier is reported only once
mdrun.c:251: error: for each function it appears in.)
mdrun.c:251: error: `cr' undeclared (first use in this function)
mdrun.c:252: error: syntax error before "fnm"
mdrun.c:284: error: syntax error before "bCart"
mdrun.c:285: error: syntax error before "bPPPME"
mdrun.c:286: error: syntax error before "bPartDec"
mdrun.c:287: error: syntax error before "bDDBondCheck"
mdrun.c:288: error: syntax error before "bDDBondComm"
mdrun.c:289: error: syntax error before "bSumEner"
mdrun.c:290: error: syntax error before "bVerbose"
mdrun.c:291: error: syntax error before "bCompact"
mdrun.c:292: error: syntax error before "bSepPot"
mdrun.c:293: error: syntax error before "bGlas"
mdrun.c:294: error: syntax error before "bIonize"
mdrun.c:295: error: syntax error before "bConfout"
mdrun.c:296: error: syntax error before "bReproducible"
mdrun.c:305: error: syntax error before "realddxyz"
mdrun.c:306: error: `ddnoNR' undeclared (first use in this function)
mdrun.c:307: warning: excess elements in scalar initializer
mdrun.c:307: warning: (near initialization for `ddno_opt')
mdrun.c:307: warning: excess elements in scalar initializer
mdrun.c:307: warning: (near initialization for `ddno_opt')
mdrun.c:307: warning: excess elements in scalar initializer
mdrun.c:307: warning: (near initialization for `ddno_opt')
mdrun.c:307: warning: excess elements in scalar initializer
mdrun.c:307: warning: (near initialization for `ddno_opt')
mdrun.c:310: error: syntax error before "rdd"
mdrun.c:312: error: syntax error before "cpt_period"
mdrun.c:313: error: syntax error before "bAppendFiles"
mdrun.c:315: error: syntax error before "pa"
mdrun.c:379: error: `gmx_edsam_t' undeclared (first use in this function)
mdrun.c:381: error: `ivec' undeclared (first use in this function)
mdrun.c:381: error: parse error before "ddxyz"
mdrun.c:383: error: `bool' undeclared (first use in this function)
mdrun.c:383: error: parse error before "HaveCheckpoint"
mdrun.c:386: error: `STRLEN' undeclared (first use in this function)
mdrun.c:388: warning: implicit declaration of function `init_par'
mdrun.c:390: warning: implicit declaration of function `MASTER'
mdrun.c:391: warning: implicit declaration of function `CopyRight'
mdrun.c:393: error: `PCA_KEEP_ARGS' undeclared (first use in this function)
mdrun.c:393: error: `PCA_NOEXIT_ON_ARGS' undeclared (first use in this
function)
mdrun.c:394: error: `PCA_CAN_SET_DEFFNM' undeclared (first use in this
function)
mdrun.c:394: error: `PCA_QUIET' undeclared (first use in this function)
mdrun.c:396: error: `gmx_parallel_env' undeclared (first use in this
function)
mdrun.c:397: error: `PCA_BE_NICE' undeclared (first use in this function)
mdrun.c:399: warning: implicit declaration of function `parse_common_args'
mdrun.c:400: warning: implicit declaration of function `asize'
mdrun.c:400: error: `fnm' undeclared (first use in this function)
mdrun.c:400: error: `pa' undeclared (first use in this function)
mdrun.c:402: warning: implicit declaration of function `nenum'
mdrun.c:407: warning: implicit declaration of function `gmx_fatal'
mdrun.c:407: error: `FARGS' undeclared (first use in this function)
mdrun.c:413: warning: implicit declaration of function `PAR'
mdrun.c:414: warning: implicit declaration of function `init_multisystem'
mdrun.c:414: error: `TRUE' undeclared (first use in this function)
mdrun.c:418: warning: implicit declaration of function `opt2bSet'
mdrun.c:420: warning: implicit declaration of function
`read_checkpoint_simulation_part'
mdrun.c:420: warning: implicit declaration of function `opt2fn'
mdrun.c:430: error: `bAppendFiles' undeclared (first use in this function)
mdrun.c:430: error: `FALSE' undeclared (first use in this function)
mdrun.c:433: error: `bAddPart' undeclared (first use in this function)
mdrun.c:446: warning: implicit declaration of function
`add_suffix_to_output_names'
mdrun.c:450: error: `MD_RERUN' undeclared (first use in this function)
mdrun.c:451: error: `bSepPot' undeclared (first use in this function)
mdrun.c:451: error: `MD_SEPPOT' undeclared (first use in this function)
mdrun.c:452: error: `bIonize' undeclared (first use in this function)
mdrun.c:452: error: `MD_IONIZE' undeclared (first use in this function)
mdrun.c:453: error: `bGlas' undeclared (first use in this function)
mdrun.c:453: error: `MD_GLAS' undeclared (first use in this function)
mdrun.c:454: error: `bPartDec' undeclared (first use in this function)
mdrun.c:454: error: `MD_PARTDEC' undeclared (first use in this function)
mdrun.c:455: error: `bDDBondCheck' undeclared (first use in this function)
mdrun.c:455: error: `MD_DDBONDCHECK' undeclared (first use in this function)
mdrun.c:456: error: `bDDBondComm' undeclared (first use in this function)
mdrun.c:456: error: `MD_DDBONDCOMM' undeclared (first use in this function)
mdrun.c:457: error: `bConfout' undeclared (first use in this function)
mdrun.c:457: error: `MD_CONFOUT' undeclared (first use in this function)
mdrun.c:458: error: `bSumEner' undeclared (first use in this function)
mdrun.c:458: error: `MD_NOGSTAT' undeclared (first use in this function)
mdrun.c:459: error: `bReproducible' undeclared (first use in this function)
mdrun.c:459: error: `MD_REPRODUCIBLE' undeclared (first use in this
function)
mdrun.c:460: error: `MD_APPENDFILES' undeclared (first use in this function)
mdrun.c:461: error: `MD_STARTFROMCPT' undeclared (first use in this
function)
mdrun.c:469: warning: implicit declaration of function `gmx_log_open'
mdrun.c:469: warning: implicit declaration of function `ftp2fn'
mdrun.c:469: error: `efLOG' undeclared (first use in this function)
mdrun.c:469: warning: assignment makes pointer from integer without a cast
mdrun.c:471: warning: implicit declaration of function `please_cite'
mdrun.c:484: error: `ed' undeclared (first use in this function)
mdrun.c:484: warning: implicit declaration of function `ed_open'
mdrun.c:488: error: `ddxyz' undeclared (first use in this function)
mdrun.c:488: error: `XX' undeclared (first use in this function)
mdrun.c:488: error: `realddxyz' undeclared (first use in this function)
mdrun.c:489: error: `YY' undeclared (first use in this function)
mdrun.c:490: error: `ZZ' undeclared (first use in this function)
mdrun.c:492: warning: implicit declaration of function `mdrunner'
mdrun.c:492: error: `bCompact' undeclared (first use in this function)
mdrun.c:493: error: `rdd' undeclared (first use in this function)
mdrun.c:493: error: `rconstr' undeclared (first use in this function)
mdrun.c:494: error: `dlb_scale' undeclared (first use in this function)
mdrun.c:495: error: `pforce' undeclared (first use in this function)
mdrun.c:496: error: `cpt_period' undeclared (first use in this function)
mdrun.c:496: error: `max_hours' undeclared (first use in this function)
mdrun.c:499: warning: implicit declaration of function `gmx_finalize'
mdrun.c:501: warning: implicit declaration of function `MULTIMASTER'
mdrun.c:502: warning: implicit declaration of function `thanx'
mdrun.c:508: warning: implicit declaration of function `gmx_log_close'
mdrun.c:306: error: storage size of `ddno_opt' isn't known
make[1]: *** [mdrun] Error 1
make[1]: Leaving directory `/cygdrive/c/tools/gromacs-4.0.4/src/kernel'
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