Fludarabine Phosphate, Clofarabine, and Busulfan With Vorinostat in Treating Patients With Acute Leukemia in Remission or Relapse Undergoing Donor Stem Cell Transplant

Inclusion Criteria: * Patients with biopsy-proven acute lymphoblastic leukemia, acute myeloid leukemia, or myelodysplastic syndrome in remission or relapse * Estimated creatinine clearance at least 50 ml/min * Bilirubin equal or less than 1.5 (unless Gilbert's syndrome) * Serum glutamate pyruvate transaminase (SGPT) \< 3 x upper limit of normal * Alkaline phosphatase \< 2 x upper limit of normal * Pulmonary function with forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC) and diffusing capacity of the lungs for carbon monoxide (DLCO) at least 45% of expected corrected for hemoglobin; children unable to perform pulmonary functions must have an oxygen saturation greater than 92% at room air * Left ventricular ejection fraction at least 45% on appropriate medical therapy; no uncontrolled arrhythmias or symptomatic cardiac disease * Zubrod performance status 0-1 or Lansky/Karnofsky performance status (PS) equal or greater to 80% * Patients must have a related, genotypically HLA identical donor, or they must have an unrelated donor who is 8/8 HLA match by high resolution typing * Patient or patient's legal representative, parent(s) or guardian should provide written informed consent; assent of a minor if participant's age is at least seven and less than eighteen years * Negative beta human chorionic gonadotropin (HCG) test in a woman with child bearing potential defined as not post-menopausal for 12 months and no previous surgical sterilization Exclusion Criteria: * Patients with active central nervous system (CNS) disease * Evidence of acute or chronic active hepatitis or cirrhosis * Uncontrolled infection, including human immunodeficiency virus (HIV), human T-lymphotropic virus (HTLV)-1, hepatitis B or hepatitis C viremia * Prior allogeneic SCT * Prior autologous SCT in last 12 months * Patients with acute myeloid leukemia (AML) in first remission after one course of induction and with favorable cytogenetics (t\[8;21\], inv 16, or t\[15;17\]) and/or molecular profile (nucleophosmin \[NPM\]1) * Prior radiation to liver in form of total body or involved field