1. дома
  2. Вопрос и ответ
  3. Aligator: Анализ пути fortran с ошибкой сегментации

Aligator: Анализ пути fortran с ошибкой сегментации

2015-02-21 2 views
-1

Я пытаюсь запустить Aligator (http://x004.psycm.uwcm.ac.uk/~peter/), но это не удается на моей 64-разрядной машине Linux. При запуске Aligator, как указано в документе-файле http://x004.psycm.uwcm.ac.uk/~peter/README_ALIGATOR.doc) Я получаю эту ошибку:Aligator: Анализ пути fortran с ошибкой сегментации

./aligator <aligator.run> out.txt 

Program received signal SIGSEGV: Segmentation fault - invalid memory reference. 

Backtrace for this error: 
#0 0x7FDCD5079577 
#1 0x7FDCD5079B7E 
#2 0x7FDCD457DCAF 
#3 0x401DBF in MAIN__ at aligator.f:? 
Segmentation fault

У меня есть ощущение, что это Fortran программное обеспечение было написано для 32-битной системы, и именно поэтому я должен был скомпилировать aligator.f так:

f77 aligator.f -mcmodel=large -o aligator

источник-код aligator.f:

CHARACTER*50 INFILE,OUTFILE 
     CHARACTER*8 PROCNAM(5),PXN 
     INTEGER JSNP(6000000,25),NSNP(6000000) 
     INTEGER ISNP(6000000) 
     INTEGER ILIS(100,2) 
     INTEGER NGS(1000000),IDSNP(1000000) 
     INTEGER IGS(1000000,25) 
     INTEGER ICH(20000),IGOC(20000) 
     INTEGER IDGE(30000),IPFC(35000,2) 
     INTEGER IDGO(20000),NGC(30000) 
     INTEGER JDGO(20000),MGC(30000) 
     INTEGER MPFC(20000),MCG(30000),NCG(30000) 
     INTEGER IGC(30000,1000),JSCO(20000) 
     INTEGER JGC(30000,1000),ISGSNP(200000) 
     INTEGER KSCO(50000,10000),MSCO(20000) 
     INTEGER NUMSIG(3,5) 
     INTEGER MUMSIG(3,5),ISLIM(200) 
     INTEGER ISCO(20000),MUM(20000),NUN(20000) 
     REAL PR(20000),CRIT(3),CUM(1000001),QR(20000) 
     REAL ZR(20000),YR(3,5),GM(20000),QZ(5),PMIN(5) 
     REAL DUM(1000001),QMIN(5) 
     REAL*8 QP(20000),CHX,RU(20000),QQ(20000) 
     REAL*8 XX,ST,YY 
     REAL*8 GETRAN 
     EXTERNAL GETRAN,QUIKSORT 
     OPEN(10,FILE='allsnp_gene_NCBI_0KB.txt') 
C  THIS FILE CONTAINS A LIST OF ALL SNPs ANNOTATED 
C  BY THE GENES THEY LIE WITHIN (NCBI ID NUMBERS) 
     OPEN(25,FILE='allsnp_gene_NCBI_0KB.list') 
     OPEN(11,FILE='gene_go_17_03_09.dat') 
     OPEN(12,FILE='pfc_17_03_09.dat') 
     READ(*,*) INFILE 
     READ(*,*) OUTFILE 
     OPEN(14,FILE=INFILE) 
     OPEN(15,FILE=OUTFILE) 
     READ(*,*) NSNPLIST 
     READ(*,*) DRIT 
     READ(*,*) NWIN 
     READ(*,*) NREP 
     READ(*,*) ST 
     NSG=5770877 
C  TOTAL NUMBER OF SNPS IN FILE allsnp_gene_NCBI_0KB.txt 
     NGO=754498 
C  TOTAL NUMBER OF GENE/GO CATEGORY ASSIGNMENTS 
     NPFC=28339 
C  TOTAL NUMBER OF GO CATEGORIES WITH NAMES/FUNCTION DATA 
     PROCNAM(1)='ALL CATS' 
     PROCNAM(2)='CELLULAR' 
     PROCNAM(3)='FUNCTION' 
     PROCNAM(4)='PROCESS ' 
     PROCNAM(5)='PRO+FUNC' 
     CRIT(1)=0.05 
     CRIT(2)=0.01 
     CRIT(3)=0.001 
     NUM=0 
     DO 873 I=1,NPFC 
     READ(12,*) (IPFC(I,K),K=1,2) 
873 CONTINUE 
     DO 871 I=1,1000000 
     NGS(I)=0 
871 CONTINUE 
     DO 872 I=1,30000 
     MGC(I)=0 
     MCG(I)=0 
872 CONTINUE 
     DO 604 I=10,99 
     READ(25,*) II,ILIS(I,1),ILIS(I,2) 
604 CONTINUE 
C  READING IN START AND END POINTS ON THE COMPLETE LIST OF SNPS WHOSE 
C  RS NUMBERS START WITH 10, 11, .... 99 
C  TO MAKE IT FASTER TO LOCATE THE SNPS USED IN A PARTICULAR STUDY. 
     MMSP=0 
     DO 503 I=1,NSG 
     READ(10,*) ISNP(I),NSNP(I),(JSNP(I,K),K=1,NSNP(I)) 
503 CONTINUE 
C  READS IN COMPLETE LIST OF SNPS WITHIN GENES 
     MGE=0 
     MSP=0 
     DO 605 I=1,NSNPLIST 
C  THIS SECTION READS IN THE SNPS USED IN THE STUDY BEING ANALYSED 
C  CHECKS THEM AGAINST THE TOTAL LIST OF SNPS WITHIN GENES 
C  TO CREATE A LIST OF SNPS WITHIN GENES AND THE GENES WITHIN WHICH THEY LIE 
     READ(14,*) II,PP 
     RS=REAL(II) 
     RX=LOG10(RS) 
     IX=INT(RX)-1 
     RJ=REAL(IX) 
     IC=INT(RS/(10**RJ)) 
     IUS=0 
     DO 696 J=ILIS(IC,1),ILIS(IC,2) 
     IF (II.EQ.ISNP(J)) THEN 
     IUS=J 
     GOTO 697 
     ENDIF 
696 CONTINUE 
697 CONTINUE 
     IF (IUS.EQ.0) THEN 
     GOTO 605 
     ENDIF 
     MSP=MSP+1 
     IDSNP(MSP)=ISNP(IUS) 
     NGS(MSP)=NSNP(IUS) 
     DO 698 J=1,NSNP(IUS) 
     JGX=JSNP(IUS,J) 
     JNE=0 
     DO 802 II=1,MGE 
     IF (JGX.EQ.IDGE(II)) THEN 
     JNE=II 
     ENDIF 
802 CONTINUE 
     IF (JNE.EQ.0) THEN 
     MGE=MGE+1 
     IDGE(MGE)=JGX 
     JNE=MGE 
     ENDIF 
     IGS(MSP,J)=JNE 
698 CONTINUE 
     IF (PP.LT.DRIT) THEN 
     NUM=NUM+1 
     ISGSNP(NUM)=MSP 
     ENDIF 
C  CREATES LIST OF SIGNIFICANT SNPS WITH P-val < SPECIFIED CRITERION 
699 CONTINUE 
605 CONTINUE 
     DUM(1)=0.0 
     DO 603 I=1,MSP 
     DUM(I+1)=DUM(I)+(1.0/FLOAT(MSP)) 
603 CONTINUE 
     DUM(MSP+1)=1.0 
     PRINT*,'SNPS READ' 
     PRINT*,'#SNPS = ',MSP 
     PRINT*,'#GENES = ',MGE 
     DO 502 I=1,NGO 
     READ(11,*) JGX,IID 
     INE=0 
     DO 842 II=1,MGE 
     IF (JGX.EQ.IDGE(II)) THEN 
     INE=II 
     GOTO 937 
     ENDIF 
842 CONTINUE 
937 CONTINUE 
     IF (INE.EQ.0) THEN 
     GOTO 502 
     ENDIF 
     JNE=0 
     DO 602 II=1,MMGO 
     IF (IID.EQ.JDGO(II)) THEN 
     JNE=II 
     ENDIF 
602 CONTINUE 
     IF (JNE.EQ.0) THEN 
     MMGO=MMGO+1 
C  PRINT*,MMGO,IID 
     JDGO(MMGO)=IID 
     JNE=MMGO 
     ENDIF 
     INF=0 
     DO 722 J=1,MGC(INE) 
     IF (JNE.EQ.JGC(INE,J)) THEN 
     INF=J 
     ENDIF 
722 CONTINUE 
     IF (INF.EQ.0) THEN 
     MGC(INE)=MGC(INE)+1 
     MCG(JNE)=MCG(JNE)+1 
     JGC(INE,MGC(INE))=JNE 
     ENDIF 
C  JGC CONTAINS ALL GO GATEGORY MEMBERSHIPS FOR EACH GENE 
502 CONTINUE 
     MGO=0 
     DO 607 I=1,MMGO 
C  THIS SECTION REMOVES GO CATEGORIES WITH FEWER THAN 3 GENES 
C  OR MORE THAN 5000 (USER CAN EDIT AND RECOMPILE IF DESIRED) 
     IF (MCG(I).LT.3.OR.MCG(I).GT.5000) THEN 
     ICH(I)=0 
     GOTO 607 
     ENDIF 
     MGO=MGO+1 
     NCG(MGO)=MCG(I) 
     IDGO(MGO)=JDGO(I) 
     ICH(I)=MGO 
     IPF=0 
     DO 874 J=1,NPFC 
     IF (IDGO(MGO).EQ.IPFC(J,1)) THEN 
     IPF=J 
     GOTO 931 
     ENDIF 
874 CONTINUE 
931 CONTINUE 
     IF (IPF.EQ.0) THEN 
     PRINT*,'MISSING CATEGORY ',IDGO(MGO) 
     ELSE 
     MPFC(MGO)=IPFC(IPF,2) 
     ENDIF 
607 CONTINUE 
     DO 609 I=1,MGE 
     NGC(I)=0 
     NGC(I)=0 
     DO 608 J=1,MGC(I) 
     JX=JGC(I,J) 
     NN=ICH(JX) 
     IF (NN.NE.0) THEN 
     NGC(I)=NGC(I)+1 
     IGC(I,NGC(I))=NN 
     ENDIF 
608 CONTINUE 
609 CONTINUE 
     PRINT*,'CATS READ' 
     PRINT*,'No.CATS = ',MGO 
     NMA=0 
     JMA=0 
     DO 226 I=1,MGE 
     IF (NGC(I).GE.NMA) THEN 
     NMA=NGC(I) 
     JMA=I 
     ENDIF 
226 CONTINUE 
     PRINT*,'MAX #CATS PER GENE = ',NMA 
     PRINT*,'GENE ID ',IDGE(JMA) 
     NMA=0 
     JMA=0 
     DO 2 I=1,MSP 
     IF (NGS(I).GE.NMA) THEN 
     NMA=NGS(I) 
     JMA=I 
     ENDIF 
2  CONTINUE 
     PRINT*,'NO. SNPS IN STUDY = ',NSNPLIST 
     PRINT*,'NO. SNPS IN GENES = ',MSP 
     PRINT*,'MAX #GENES PER SNP = ',NMA 
     PRINT*,'SNP ID ',IDSNP(JMA) 
     NMA=0 
     JMA=0 
     DO 3 I=1,MGO 
     IF (NGC(I).GE.NMA) THEN 
     NMA=NGC(I) 
     JMA=I 
     ENDIF 
3  CONTINUE 
     DO 987 IY=1,20000 
     ISCO(IY)=0 
     JSCO(IY)=0 
987 CONTINUE 
     DO 587 IY=1,3 
     DO 787 IZ=1,5 
     NUMSIG(IY,IZ)=0 
787 CONTINUE 
587 CONTINUE 
     JGE=0 
     DO 14 I=1,NUM 
     DO 198 J=1,20000 
     IGOC(J)=0 
198 CONTINUE 
     KU=ISGSNP(I) 
C  GET THE ID OF EACH SIGNIFICANT SNP 
     DO 16 J=1,NGS(KU) 
     ICG=IGS(KU,J) 
C  WHAT GENES DOES IT LIE IN ? 
     IUS=0 
     DO 26 K=1,JGE 
     IF (ICG.EQ.JSCO(K)) THEN 
     IUS=K 
     ENDIF 
26 CONTINUE 
C  IS THIS GENE ALREADY ON THE LIST ? 
     IF (IUS.EQ.0) THEN 
     JGE=JGE+1 
     JSCO(JGE)=ICG 
C  ADD GENE TO LIST 
     DO 18 KK=1,NGC(ICG) 
     K=IGC(ICG,KK) 
     IF (IGOC(K).EQ.0) THEN 
      ISCO(K)=ISCO(K)+1 
      IGOC(K)=1 
     ENDIF 
C  INCREASE THE COUNT OF SIGNIFICANT GENES FOR ALL GO CATEGORIES 
C  CONTAINING THIS GENE BY 1 - BUT ONLY IF THIS SNP HASN'T ALREADY 
C  CONTRIBUTED A GENE TO THIS CATEGORY. IF A SNP LIES 
C  IN SEVERAL OVERLAPPING GENES ALL IN THE SAME GO CATEGORY, 
C  THIS PREVENTS ALL THE GENES BEING COUNTED SEPARATELY. 
18  CONTINUE 
     ENDIF 
16 CONTINUE 
14 CONTINUE 
     PRINT*,'P-VALUE CRITERION FOR DEFINING SIGNIFICANT SNPS = ',DRIT 
     PRINT*,'NUMBER OF GENES WITH SIGNIFICANT SNPS = ',JGE 
     PRINT*,'NUMBER OF SIMULATED REPLICATE GENE-LISTS = ',NWIN 
     PRINT*,'NUMBER OF BOOTSTRAP STUDIES = ',NREP 
     DO 979 IT=1,NWIN 
     PRINT*,'SIMULATED REPLICATE GENELIST',IT 
     KRE=1 
     DO 887 IY=1,10000 
     JSCO(IY)=0 
     GM(IY)=0 
     KSCO(IT,IY)=0 
887 CONTINUE 
     KGE=0 
666 CONTINUE 
     YY=GETRAN(XX,ST) 
     R=REAL(XX) 
     KU=0 
     DO 551 K=1,MSP 
     IF (R.GE.DUM(K).AND.R.LT.DUM(K+1)) THEN 
     KU=K 
     ENDIF 
551 CONTINUE 
C  SELECT A RANDOM SNP 
     DO 298 J=1,20000 
     IGOC(J)=0 
298 CONTINUE 
     DO 116 J=1,NGS(KU) 
     ICG=IGS(KU,J) 
C  WHAT GENES DOES THE SNP LIE IN ? 
     IUS=0 
     DO 216 K=1,KGE 
     IF (ICG.EQ.JSCO(K)) THEN 
     IUS=K 
     ENDIF 
216 CONTINUE 
C  GENE ALREADY ON LIST ? 
C  PRINT*,II,NID-I,IDJ,IUS,ICG 
     IF (IUS.EQ.0) THEN 
     KGE=KGE+1 
C  PRINT*,IT,KGE 
     IF (KGE.GT.JGE) THEN 
      GOTO 994 
     ENDIF 
C  GENELIST REACHED THE SAME LENGTH AS THE ORIGINAL ? 
     JSCO(KGE)=ICG 
     DO 118 KK=1,NGC(ICG) 
     K=IGC(ICG,KK) 
     IF (IGOC(K).EQ.0) THEN 
      KSCO(IT,K)=KSCO(IT,K)+1 
      IGOC(K)=1 
     ENDIF 
118  CONTINUE 
C  ADD 1 TO EACH GO CATEGORY CONTAINING THE GENE (SEE ABOVE) 
     ENDIF 
116 CONTINUE 
     GOTO 666 
994 CONTINUE 
979 CONTINUE 
     DO 812 IX=1,5 
     PMIN(IX)=99.0 
812 CONTINUE 
     NSCA=0 
     DO 22 I=1,MGO 
     NMP=MPFC(I) 
     IF (ISCO(I).LE.1) THEN 
     GOTO 22 
     ENDIF 
C  ONLY COUNT GO CATEGORIES WITH TWO OR MORE SIGNIFICANT GENES 
     PR(I)=0 
     ZR(I)=0 
     RU(I)=0.0d0 
     CUM(1)=0 
     DO 32 J=1,NWIN 
     IF (ISCO(I).LE.KSCO(J,I)) THEN 
     PR(I)=PR(I)+(1.0/FLOAT(NWIN)) 
     ENDIF 
C  CATEGORY-SPECIFIC P-VALUE = NUMBER OF SIMULATED GENELISTS 
C  WHERE THE SCORE FOR THE CATEGORY (KSCO) IS AT LEAST AS HIGH 
C  AS THAT IN THE REAL DATA (ISCO) 
     CUM(J+1)=CUM(J)+(1.0/FLOAT(NWIN)) 
     GM(I)=GM(I)+(FLOAT(KSCO(J,I))/FLOAT(NWIN)) 
C  CALCULATING EXPECTED NUMBER OF SIGNIFICANT GENES IN THE CATEGORY 
32 CONTINUE 
     CUM(NWIN+1)=1.0 
     IF (PR(I).LT.PMIN(1)) THEN 
     PMIN(1)=PR(I) 
     ENDIF 
     DO 813 J=1,3 
     IF (NMP.EQ.J.AND.PR(I).LE.PMIN(J+1)) THEN 
     PMIN(J+1)=PR(I) 
     ENDIF 
813 CONTINUE 
     IF (NMP.GE.2.AND.PR(I).LE.PMIN(5)) THEN 
     PMIN(5)=PR(I) 
     ENDIF 
C  CALCULATING MINIMUM P-VALUES FOR CATEGORIES OF EACH FUNCTIONAL TYPE 
     DO 33 J=1,3 
     IF (PR(I).LE.CRIT(J)) THEN 
     NUMSIG(J,1)=NUMSIG(J,1)+1 
     NUMSIG(J,NMP+1)=NUMSIG(J,NMP+1)+1 
     IF (NMP.GE.2) THEN 
      NUMSIG(J,5)=NUMSIG(J,5)+1 
     ENDIF 
     ENDIF 
C  COUNTING NUMBER OF CATEGORIES REACHING A GIVEN CATEGORY-SPECIFIC P-VALUE 
33 CONTINUE 
     QP(I)=DBLE(PR(I)) 
22 CONTINUE 
     NBOOT=NWIN 
     DO 716 IC=1,3 
     DO 816 ID=1,5 
     YR(IC,ID)=0 
816 CONTINUE 
716 CONTINUE 
     DO 819 I=1,5 
     QZ(I)=0 
819 CONTINUE 
     DO 51 I=1,NREP 
C  PRINT*,I 
C  PERFORMING REPLICATE "STUDIES" TO GET SIGNIFICANCE OF NUMBERS OF 
C  SIGNIFICANTLY OVER-REPRESENTED CATEGORIES 
     YY=GETRAN(XX,ST) 
     R=REAL(XX) 
     IYS=0 
     DO 53 K=1,NWIN 
     IF (R.GE.CUM(K).AND.R.LT.CUM(K+1)) THEN 
     IYS=K 
     ENDIF 
53 CONTINUE 
C  CHOOSE A REPLICATE GENE-LIST TO ACT AS THE "REAL DATA" 
     DO 54 K=1,MGO 
     MSCO(K)=KSCO(IYS,K) 
     QR(K)=0 
54 CONTINUE 
     DO 58 K=1,3 
     DO 589 KK=1,5 
     MUMSIG(K,KK)=0 
589 CONTINUE 
58 CONTINUE 
     DO 52 J=1,NBOOT 
528 CONTINUE 
     YY=GETRAN(XX,ST) 
     R=REAL(XX) 
     JYS=0 
     DO 55 K=1,NWIN 
     IF (R.GE.CUM(K).AND.R.LT.CUM(K+1)) THEN 
     JYS=K 
     ENDIF 
55 CONTINUE 
     IF (JYS.EQ.IYS) THEN 
     GOTO 528 
     ENDIF 
C  SELECT REPLICATE GENE LISTS (WITH REPLACEMENT) 
     DO 56 K=1,MGO 
     IF (MSCO(K).LE.KSCO(JYS,K)) THEN 
     QR(K)=QR(K)+(1.0/FLOAT(NBOOT)) 
     ENDIF 
C  OBTAIN CATEGORY-SPECIFIC P-VALUES FOR THE "REAL DATA" 
56 CONTINUE 
52 CONTINUE 
     DO 814 K=1,5 
     QMIN(K)=99.0 
814 CONTINUE 
     DO 57 K=1,MGO 
     NMP=MPFC(K) 
     IF (MSCO(K).LE.1) THEN 
     GOTO 57 
     ENDIF 
     JGG=IDGO(K) 
     IF (QR(K).LT.QMIN(1)) THEN 
     QMIN(1)=QR(K) 
     ENDIF 
     DO 815 JX=1,3 
     IF (NMP.EQ.JX.AND.QR(K).LE.QMIN(JX+1)) THEN 
     QMIN(JX+1)=QR(K) 
     ENDIF 
815 CONTINUE 
     IF (NMP.GE.2.AND.QR(K).LE.QMIN(5)) THEN 
     QMIN(5)=QR(K) 
     ENDIF 
C  OBTAIN MINIMUM P-VALUES FOR CATEGORIES OF VARIOUS FUNCTIONAL TYPES 
     DO 63 JJ=1,3 
     IF (QR(K).LE.CRIT(JJ)) THEN 
     MUMSIG(JJ,1)=MUMSIG(JJ,1)+1 
     MUMSIG(JJ,NMP+1)=MUMSIG(JJ,NMP+1)+1 
     IF (NMP.GE.2) THEN 
      MUMSIG(JJ,5)=MUMSIG(JJ,5)+1 
     ENDIF 
     ENDIF 
C  OBTAIN NUMBERS OF CATEGORIES WITH CATEGORY-SPECIFIC P-VALUES LESS THAN 
C  VARIOUS CRITERIA 
63 CONTINUE 
57 CONTINUE 
     DO 67 K=1,MGO 
     IF (ISCO(K).LE.1) THEN 
     GOTO 67 
     ENDIF 
     IF (PR(K).GE.QMIN(1)) THEN 
     ZR(K)=ZR(K)+(1.0/FLOAT(NREP)) 
     ENDIF 
C  PROBABILITY THAT ANY CATEGORY-SPECIFIC P-VALUE IN A STUDY WHERE THERE 
C  IS NO FUNCTIONAL ASSOCIATION (i.e. RANDOMLY-SELECTED "REAL DATA") IS 
C  LESS THAN OR EQUAL TO THE P-VALUE OF A GIVEN CATEGORY IN THE ORIGINAL 
C  DATASET (i.e. A STUDY-WIDE P-VALUE CORRECTED FOR TESTING MULTIPLE NON- 
C  INDEPENDENT CATEGORIES) 
     DO 77 KK=1,MGO 
     IF (MSCO(KK).LE.1) THEN 
     GOTO 77 
     ENDIF 
     IF (PR(K).GE.QR(KK)) THEN 
     RU(K)=RU(K)+(1.0d0/DFLOAT(NREP)) 
     ENDIF 
C  EXPECTED NUMBER OF CATEGORIES PER STUDY WITH CATEGORY-SPECIFIC P-vALUES 
C  LESS THAN OR EQUAL TO THAT OF A GIVEN CATEGORY IN THE ORIGINAL DATASET 
77 CONTINUE 
67 CONTINUE 
     DO 817 JJ=1,5 
     IF (QMIN(JJ).LE.PMIN(JJ)) THEN 
     QZ(JJ)=QZ(JJ)+(1.0/FLOAT(NREP)) 
     ENDIF 
C  PROBABILITY THAT THE MINIMUM CATEGORY-SPECIFIC P-VALUE IN A STUDY WHERE THERE 
C  IS NO FUNCTIONAL ASSOCIATION (i.e. RANDOMLY-SELECTED "REAL DATA") IS 
C  LESS THAN OR EQUAL TO THE MINIMUM CATEGORY-SPECIFIC P-VALUE IN THE ORIGINAL 
C  DATA 
817 CONTINUE 
     DO 64 JJ=1,3 
     DO 642 JH=1,5 
     IF (MUMSIG(JJ,JH).GE.NUMSIG(JJ,JH)) THEN 
     YR(JJ,JH)=YR(JJ,JH)+(1.0/FLOAT(NREP)) 
     ENDIF 
C  PROBABILITY THAN THE NUMBER OF CATEGORIES REACHING SIGNIFICANCE IN A STUDY 
C  WHERE THERE IS NO FUNCTIONAL ASSOCIATION (i.e. RANDOMLY-SELECTED "REAL DATA") 
C  IS LESS THAN OR EQUAL TO THAT IN THE ORIGINAL DATA (i.e. TESTING FOR A 
C  SIGNIFICANTLY LARGE NUMBER OF OVER-REPRESENTED CATEGORIES) 
642 CONTINUE 
64 CONTINUE 
51 CONTINUE 
     DO 712 IT=1,MGO 
     IF (ISCO(IT).EQ.0) THEN 
     QP(IT)=1d0+DBLE(GM(IT)) 
     ENDIF 
712 CONTINUE 
     X=QUIKSORT(QP,MGO,MUM) 
     DO 23 I=1,MGO 
     J=MUM(I) 
     NMP=MPFC(J) 
     PXN=PROCNAM(NMP+1) 
     JG=IDGO(J) 
     JH=ISCO(J) 
     IF (ISCO(J).LE.1) THEN 
     GOTO 23 
     ENDIF 
C  ONLY COUNT GO CATEGORIES WITH TWO OR MORE SIGNIFICANT GENES 
     WRITE(15,44) JG,PXN,JH,JGE,NCG(J),MGE,GM(J),PR(J),ZR(J),RU(J) 
23 CONTINUE 
     WRITE(15,*) 
     WRITE(15,*) 
     DO 691 ISS=1,5 
     WRITE(15,*) PROCNAM(ISS) 
     WRITE(15,*) 
     WRITE(15,*) 'MIN P =',PMIN(ISS),' SIG = ',QZ(ISS) 
     WRITE(15,*) 
     DO 69 IS=1,3 
     WRITE(15,*) 'NO. OF P<',CRIT(IS),' =',NUMSIG(IS,ISS) 
     WRITE(15,*) 'SIG = ',YR(IS,ISS) 
69 CONTINUE 
     WRITE(15,*) 
691 CONTINUE 
     CLOSE(15) 
44 FORMAT(I8,2X,A8,3(2X,I5),2X,I5,2X,F7.2,2X,F7.5,2X,F6.4,2X,F9.2) 
     STOP 
     END 

     REAL*8 FUNCTION GETRAN(X,S) 
     REAL*8 X,S,A,B,SN,SS,RN 
     INTEGER IS 
     A=7D0**5 
     B=(2D0**31)-1 
     SN=S*A 
     IS=INT(SN/B) 
     SS=DFLOAT(IS) 
C  PRINT*,SN,SS,IS 
     RN=SN-(SS*B) 
     S=RN 
     X=S/B 
     GETRAN=1D0 
     RETURN 
     END 

     REAL FUNCTION QUIKSORT(RLOD,NLO,NUM) 
     REAL*8 RLOD(20000) 
     REAL*8 SORT1(20000),SORT2(20000),SORT3(20000) 
     INTEGER NUM(20000),NUM1(20000),NUM2(20000) 
     DO 5 I=1,NLO 
     SORT1(I)=-1000.0D0 
     NUM1(I)=0 
5  CONTINUE 
     DO 10 I=1,NLO 
     XLO=RLOD(I) 
C  PRINT*,XLO 
     DO 20 J=NLO+1-I,NLO 
     IF (XLO.GE.SORT1(J)) THEN 
C  PRINT*,XLO,SORT1(J),J 
     IPOS=J 
     ENDIF 
20 CONTINUE 
C  PRINT*,IPOS 
     SORT2(IPOS)=XLO 
     NUM2(IPOS)=I 
     DO 30 K=2,IPOS 
     SORT2(K-1)=SORT1(K) 
     NUM2(K-1)=NUM1(K) 
30 CONTINUE 
     DO 40 K=IPOS+1,NLO 
     SORT2(K)=SORT1(K) 
     NUM2(K)=NUM1(K) 
40 CONTINUE 
     DO 50 L=1,NLO 
     NUM1(L)=NUM2(L) 
     SORT1(L)=SORT2(L) 
C  PRINT*,L,SORT1(L) 
50 CONTINUE 
10 CONTINUE 
     DO 60 I=1,NLO 
     NUM(I)=NUM1(I) 
60 CONTINUE 
     QUIKSORT=1.0 
     RETURN 
     END

Потому что я не Фортран-кодировщик, я задаюсь вопросом, если этот код может быть изменен, чтобы полностью s Поддерживает 64-битную систему?

EDIT: Я попытался компиляции, как это:

gfortran aligator.f -o aligator -g -fcheck=all -fbacktrace

с этими ошибками:

/tmp/ccbJsCPS.o: In function `MAIN__': 
/home/alexsson/Programs/Aligator/aligator.f:354:(.text+0x628a): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:355:(.text+0x62ff): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:356:(.text+0x6374): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:357:(.text+0x6380): relocation truncated to fit: R_X86_64_PC32 against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:360:(.text+0x65c5): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:360:(.text+0x65eb): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:365:(.text+0x66c3): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:365:(.text+0x66e9): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:369:(.text+0x697d): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:370:(.text+0x69ee): relocation truncated to fit: R_X86_64_32S against `.bss' 
/home/alexsson/Programs/Aligator/aligator.f:371:(.text+0x6a6a): additional relocation overflows omitted from the output 
collect2: error: ld returned 1 exit status

Я не уверен, если я умнее ...

Решение : Благодаря tkoenig решение является cha nge исходный код aligator.f к этому: http://pastebin.com/tnYhuba3

Он работает на моей 64-разрядной системе Slackware (с поддержкой Multilib) с 16 ГБ оперативной памяти.

источник

2015-02-21 user1261558

+0

Скомпилируйте новый компилятор gfortran с параметрами '-g -fcheck = all -fbacktrace' и запустите полученную программу. Это даст вам более ясное сообщение об ошибке, по крайней мере –

+0

Привет, спасибо за предложение, пожалуйста, см. Мой пост выше для получения результатов. – user1261558

ответ

1

У вас есть действительно больших массивов там, которые вызывают проблемы с 32-разрядным режимом адресации. Если вы делаете массивы размещаемыми и выделить их в начале программы, как и с

CHARACTER*50 INFILE,OUTFILE 
    CHARACTER*8 PROCNAM(5),PXN 
    integer, dimension(:,:), allocatable :: jsnp 
    integer, dimension(:), allocatable :: nsnp, isnp 
    INTEGER ILIS(100,2) 
    INTEGER NGS(1000000),IDSNP(1000000) 
    INTEGER IGS(1000000,25) 
    INTEGER ICH(20000),IGOC(20000) 
    INTEGER IDGE(30000),IPFC(35000,2) 
    INTEGER IDGO(20000),NGC(30000) 
    INTEGER JDGO(20000),MGC(30000) 
    INTEGER MPFC(20000),MCG(30000),NCG(30000) 
    integer, dimension(:,:), allocatable :: igc, jgc, ksco 
    INTEGER JSCO(20000) 
    INTEGER ISGSNP(200000) 
    INTEGER MSCO(20000) 
    INTEGER NUMSIG(3,5) 
    INTEGER MUMSIG(3,5),ISLIM(200) 
    INTEGER ISCO(20000),MUM(20000),NUN(20000) 
    REAL PR(20000),CRIT(3),CUM(1000001),QR(20000) 
    REAL ZR(20000),YR(3,5),GM(20000),QZ(5),PMIN(5) 
    REAL DUM(1000001),QMIN(5) 
    REAL*8 QP(20000),CHX,RU(20000),QQ(20000) 
    REAL*8 XX,ST,YY 
    REAL*8 GETRAN 
    EXTERNAL GETRAN,QUIKSORT 
    allocate(JSNP(6000000,25)) 
    allocate(NSNP(6000000), ISNP(6000000)) 
    allocate(IGC(30000,1000),JGC(30000,1000),KSCO(50000,10000))

это больше не должно быть проблемой.

Не могу проверить это из-за нехватки памяти.

В зависимости от диапазона значений, которые необходимо использовать для INTEGER, это также может быть интересно изменить целое число по умолчанию для двухбайтного или один байт типа, как и в

integer, parameter :: i2 = selected_int_kind(4) ! select range of at least 10000, usually translates into two bytes 
    integer(kind=i2), dimension(:,:), allocatable :: jsnp

или

integer, parameter :: i1 = selected_int_kind(2) ! one-byte integer

Это может привести к значительной экономии памяти и скорости.

источник

2015-02-21 12:00:49

+0

Спасибо. Я мог бы скомпилировать aligator без mcmodel-flag. Тем не менее, я все еще получаю ту же ошибку при ее запуске ... Это программное обеспечение кажется безнадежным. – user1261558

+0

Если я изменяю целое число на два байта, я получаю следующее: В строке 79 файла aligator.f (unit = 10, file = 'allsnp_gene_NCBI_0KB.txt ') Ошибка выполнения Fortran: целочисленное переполнение при чтении элемента 1 – user1261558

+0

Строка 79: READ (10, *) ISNP (I), NSNP (I), (JSNP (I, K), K = 1, NSNP (I)) – user1261558

Смежные вопросы

 Смежные вопросы