Where does the Gra mention the idea that Sefer Devarim is split up into parshiot representing the centuries going into the 6000 millennium? There is another idea that Ki Tavo fits into the years of the holocaust,where is this idea from?
The first idea was stated in the name of the Gra by R' Hayyim of Volozhin, who mentioned it to Rav Yitzhak Margoliot, who mentioned it to R' Shmuel ben Avraham of Slutzk, who published it in a collection of sayings of the Gra (Koenigsburg, 1864). My source for that is HaMeor HaGadol (המאור הגדול: הגאון החסיד מווילנא זללה"ה), published in two volumes by יששכר דוב קרויזר (Makhon Moreshet haGra: Jerusalem, 2004).
In volume 1, the second comment appended to Deuteronomy 25:15 reads as follows (this is a direct quote from R' Shmuel ben Avraham's sefer):
ושמעתי מפי הרה"ג הישיש וכו' מו"ה יצחק מרגליות, אב"ד בשצוצין במדינת פולין, ששמע מפי מאור הגולה מהר"ח מוואלזין ז"ל, כי הגר"א ז"ל אמר, כי בספר 'משנה תורה' מרומז בכל סדרה מה שיארע במאה שנים מאלף השישי, כסדר יו"ד פרשיות נגד יו"ד מאות, כי "נצבים וילך" נחשבים לאחד כידוע
ושאל לו מהר"ח: איה איפה אנו מרומזים בפרשת 'כי תצא', שהוא נגד המאה הששית שאנחנו עומדים כעת. והשיב לו, כי שמו מרומז בתיבת "אבן שלמה" כנ"ל, ושם מהר"ח נעלם ממנו. (לא פורש אם הגר"א העלים ממהר"ח, או מהר"ח העלים מהשומעים מפני רוב ענותנותו. ולפי זה דעה לנבון נקל, כי הרעות רבות וצרות אשר השיגונו בעו"ה במאה השביעית הזאת, מרומזים בקללות שבפרשת 'כי תבא' ודו"ק), ועתה נצפה לגאולה העתידה במהרה בימימנו אמן
I heard from R' Yitzhak Margoliot, the av beit din of Szczecin, who heard it from R' Hayyim of Volozhin, that the Gra said that the book of Deuteronomy alludes in each parsha to what will occur in each century of the sixth millennium, for the ten parshas correspond to the ten centuries (Nitzavim and Vayyelekh being considered as one, as is known).
R' Hayyim asked him where, therefore, the two of them were alluded to in Parshat Ki Teitze, which corresponds to the sixth century, in which they were currently situated. [The Gra was born about 5480. This conversation took place during the sixth century of the sixth millennium - ie: after 5500]. He answered him that his own name was alluded to in the words "אבן שלמה" [ie: אליהו בן שלמה זלמן], but the name of R' Hayyim was hidden from him. (He did not clarify whether the Gra hid it from R' Hayyim or R' Hayyim hid it from those listening, due to his tremendous humility. But because of this, wisdom comes easily to the discerning, that the great and vexatious evils that overtook us in this world, in this seventh century, were alluded to in the curses of Parshat Ki Tavo), and now we anticipate the future redemption, speedily and in our days. Amen.
I do not know to which events R' Shmuel ben Avraham is alluding, since for them to take place within the seventh century and to precede the publication of his text they would need to transpire between 1840 and 1864. It may have been the second of the Odessa pogroms in 1859 that he had in mind. In any case, if we were to utilise the same schema, only the first six years of the Shoah (1933-1939, or 5693-5699) would correspond to Ki Tavo. The events of 1940-1945 (5670-5675) would correspond to Parshat Nitzavim/Vayyelekh instead.
Speaking for myself, I have not heard this particular idea before anyway, and I wonder if it might be possible that you are confusing Parshat Ki Tavo with Parshat Bechukotai? If so, the source for your idea may be what R' Meir Simcha of Dvinsk says in Meshekh Chokhma, on Leviticus 26:44. It's too lengthy to quote in full, but he speaks of the nature of the exile as being one in which people become accustomed to where they are, as a result of which God causes a great storm to come and violently uproot them, reminding them all that they are Jews.
A little way into this discussion, he relates these warnings specifically to those Jews who desist from learning their laws, who learn languages not their own, who engage in ways of destruction and not in ways of reparation, and who consider Berlin to be Jerusalem (יחשוב כי ברלין היא ירושלים). He then promises another storm of terrible proportions, which you can read inside for yourself.